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Sign up| #' Write simulated data into formats used by standard GWAS software. | |
| #' | |
| #' writeStandardOutput can write genotypes and phenotypes as well as possible | |
| #' covariates and kinship matrices into a number of formats for standard GWAS | |
| #' software: plink, snptest, bimbam, gemma, limmbo. For more information on the | |
| #' different file formats see \emph{External formats}. | |
| #' | |
| #' @param genotypes [NrSamples x NrSNP] Data.frame/matrix of genotypes | |
| #' [integers]/[doubles]. | |
| #' @param phenotypes [NrSamples x NrTrait] Data.frame/matrix of phenotypes | |
| #' [doubles]. | |
| #' @param additionalPhenotypes [NrSamples x NrTrait] Data.frame/matrix of | |
| #' additional phenotypes (for instance non-linearly tranformed orginal | |
| # phenotypes via runSimulation) [doubles]. | |
| #' @param covariates [NrSamples x NrCovariates] Data.frame/matrix of covariates | |
| #' [integers]/[doubles]. | |
| #' @param kinship [NrSamples x NrSamples] Data.frame/matrix of kinship estimates | |
| #' [doubles]. | |
| #' @param eval_kinship [NrSamples] vector with eigenvalues of kinship matrix | |
| #' [doubles]. | |
| #' @param evec_kinship [NrSamples x NrSamples] Data.frame/matrix with | |
| #' eigenvectors of kinship matrix [doubles]. | |
| #' @param format Vector of name(s) [string] of file formats, options are: | |
| #' "plink", "snptest", "gemma", "bimbam", "delim". For details on the file | |
| #' formats see \emph{External formats}. | |
| #' @param id_samples Vector of [NrSamples] sample IDs [string] of simulated | |
| #' phenotypes, genotypes and covariates. | |
| #' @param id_snps Vector of [NrSNPs] SNP IDs [string] of (simulated) | |
| #' genotypes. | |
| #' @param id_phenos Vector of [NrTraits] phenotype IDs [string] of | |
| #' simulated phenotypes. | |
| #' @param standardInput_samples (optional) Data.frame of sample information | |
| #' obtained when genotypes were read from plink, oxgen or genome file. | |
| #' @param standardInput_genotypes (optional) Data.frame of genotypes obtained | |
| #' when reading genotypes from plink, oxgen, or genome file. | |
| #' @param directory Absolute path (no tilde expansion) to parent directory | |
| #' [string] where the data should be saved [needs user writing permission] | |
| #' @param outstring (optional) Name [string] of subdirectory (in relation to | |
| #' directory) to save set-up independent simulation results. | |
| #' @param intercept_gemma [boolean] When modeling an intercept term in gemma, a | |
| #' column of 1's have to be appended to the covariate files. Set intercept_gemma | |
| #' to TRUE to include a column of 1's in the output. | |
| #' @param nameAdditional name [string] of additonal phenotypes to be appended to | |
| #' filename. | |
| #' @param verbose [boolean]; If TRUE, progress info is printed to standard out | |
| #' @section External formats: | |
| #' \itemize{ | |
| #' \item plink format: consists of three files, .bed, .bim and .fam. | |
| #' From \url{https://www.cog-genomics.org/plink/1.9/formats}: The .bed | |
| #' files contain the primary representation of genotype calls at biallelic | |
| #' variants in a binary format. The .bim is a text file with no header | |
| #' line, and one line per variant with the following six fields: i) Chromosome | |
| #' code (either an integer, or 'X'/'Y'/'XY'/'MT'; '0' indicates unknown) or | |
| #' name, ii) Variant identifier, iii) Position in morgans or centimorgans (safe | |
| #' to use dummy value of '0'), iv) Base-pair coordinate (normally 1-based, but | |
| #' 0 ok; limited to 231-2), v) Allele 1 (corresponding to clear bits in .bed; | |
| #' usually minor), vi) Allele 2 (corresponding to set bits in .bed; usually | |
| #' major). The .fam file is a text file with no header line, and one line per | |
| #' sample with the following six fields: i) Family ID ('FID'), ii), Within- | |
| #' family ID ('IID'; cannot be '0'), iii) Within-family ID of father ('0' if | |
| #' father isn't in dataset, iv) within-family ID of mother ('0' if mother isn't | |
| #' in dataset), v) sex code ('1' = male, '2' = female, '0' = unknown), vi) | |
| #' Phenotype value ('1' = control, '2' = case, '-9'/'0'/non-numeric = missing | |
| #' data if case/control) | |
| #' \item snptest format: consists of two files, the genotype file ending in .gen | |
| #' (genotypes_snptest.gen) and the sample file ending in .sample | |
| #' (Ysim_snptest.sample). From | |
| #' \url{https://www.well.ox.ac.uk/~gav/snptest/#input_file_formats}: | |
| #' The genotype file stores data on a one-line-per-SNP format. The first 5 | |
| #' entries of each line should be the SNP ID, RS ID of the SNP, base-pair | |
| #' position of the SNP, the allele coded A and the allele coded B. The SNP ID | |
| #' can be used to denote the chromosome number of each SNP. The next three | |
| #' numbers on the line should be the probabilities of the three genotypes AA, | |
| #' AB and BB at the SNP for the first individual in the cohort. The next three | |
| #' numbers should be the genotype probabilities for the second individual in the | |
| #' cohort. The next three numbers are for the third individual and so on. The | |
| #' order of individuals in the genotype file should match the order of the | |
| #' individuals in the sample file. The sample file has three parts (a) a header | |
| #' line detailing the names of the columns in the file, (b) a line detailing the | |
| #' types of variables stored in each column, and (c) a line for each individual | |
| #' detailing the information for that individual. | |
| #' a) The header line needs a minimum of three entries. The first three entries | |
| #' should always be ID_1, ID_2 and missing. They denote that the first three | |
| #' columns contain the first ID, second ID and missing data proportion of each | |
| #' individual. Additional entries on this line should be the names of covariates | |
| #' or phenotypes that are included in the file. In the above example, there are | |
| #' 4 covariates named cov_1, cov_2, cov_3, cov_4, a continuous phenotype named | |
| #' pheno1 and a binary phenotype named bin1. All phenotypes should appear after | |
| #' the covariates in this file. b) The second line (the variable type line) | |
| #' details the type of variables included in each column. The first three | |
| #' entries of this line should be set to 0. Subsequent entries in this line for | |
| #' covariates and phenotypes should be specified by the following rules: D for | |
| #' Discrete covariates (coded using positive integers), C for Continuous | |
| #' covariates, P for Continuous Phenotype, B for Binary Phenotype (0 = Controls, | |
| #' 1 = Cases). c) Individual information: one line for each individual | |
| #' containing the information specified by the entries of the header line. | |
| #' Entries of the sample file are separated by spaces. | |
| #' \item bimbam format: consists of a) a simple, tab-separated phenotype file | |
| #' without sample or phenotype header/index (Ysim_bimbam.txt) and b) the mean | |
| #' genotype file format which is a single file, without information on individuals: | |
| #' (genotypes.bimbam). From \url{http://www.haplotype.org/bimbam.html}: | |
| #' The first column of the mean genotype files is the SNP ID, the second and | |
| #' third columns are allele types with minor allele first. The rest columns are | |
| #' the mean genotypes of different individuals – numbers between 0 and 2 that | |
| #' represents the (posterior) mean genotype, or dosage of the minor allele. | |
| #' \item gemma format: consists of a) a simple, tab-separated phenotype file | |
| #' without sample or phenotype header/index (Ysim_gemma.txt) and b) the mean | |
| #' genotype file format which is a single file, without information on | |
| #' individuals(genotypes.gemma); a) and b) both the same as above for bimbam | |
| #' format). In addition and if applicable, c) a kinship file (kinship_gemma.txt) | |
| #' and d) covariate file (Covs_gemma.txt). From | |
| #' \url{http://www.xzlab.org/software/GEMMAmanual.pdf}: The kinship file | |
| #' contains a NrSample × NrSample matrix, where each row and each column | |
| #' corresponds to individuals in the same order as in the mean genotype file, | |
| #' and ith row and jth column is a number indicating the relatedness value | |
| #' between ith and jth individuals. The covariates file has the same format as | |
| #' the phenotype file dsecribed above and must contain a column of 1’s if one | |
| #' wants to include an intercept term (set parameter intercept_gemma=TRUE). | |
| #' \item limmbo format: consists of a) a comma-separated phenotype file | |
| #' without sample IDs as index and phenotype IDs as header (Ysim_limmbo.csv), | |
| #' b) the mean genotype file format with one genetic variant per line. The | |
| #' first column contains the variant ID, column 2-N+1 contain the genotype code | |
| #' (numbers between 0 and 2 that represent the (posterior) mean genotype/dosage | |
| #' of the minor allele) for N samples, c) a kinship file (kinship_limmbo.csv) | |
| #' and d) covariate file (covs_limmbo.csv). From | |
| #' | |
| #' } | |
| #' @export | |
| #' @seealso \link{readStandardGenotypes} | |
| #' @examples | |
| #' simulation <- runSimulation(N=10, P=2, genVar=0.4, h2s=0.2, phi=1) | |
| #' genotypes <- simulation$rawComponents$genotypes | |
| #' kinship <- simulation$rawComponents$kinship | |
| #' phenotypes <- simulation$phenoComponents$Y | |
| #' | |
| #' \dontrun{ | |
| #' # Save in plink format (.bed, .bim, .fam, Y_sim_plink.txt) | |
| #' writeStandardOutput(directory=tempdir(), | |
| #' genotypes=genotypes$genotypes, phenotypes=phenotypes, | |
| #' id_samples = genotypes$id_samples, id_snps = genotypes$id_snps, | |
| #' id_phenos = colnames(phenotypes), format="plink") | |
| #' | |
| #' # Save in gemma and snptest format | |
| #' writeStandardOutput(directory=tempdir(), | |
| #' genotypes=genotypes$genotypes, phenotypes=phenotypes, | |
| #' id_samples = genotypes$id_samples, id_snps = genotypes$id_snps, | |
| #' id_phenos = colnames(phenotypes), kinship=kinship, | |
| #' format=c("snptest", "gemma")) | |
| #' } | |
| writeStandardOutput <- function(directory, phenotypes=NULL, | |
| genotypes=NULL, | |
| additionalPhenotypes=NULL, | |
| covariates=NULL, kinship=NULL, | |
| eval_kinship=NULL, evec_kinship=NULL, | |
| id_samples, id_snps, id_phenos, | |
| outstring=NULL, | |
| standardInput_samples=NULL, | |
| standardInput_genotypes=NULL, | |
| format = NULL, | |
| intercept_gemma=FALSE, | |
| nameAdditional="_nonLinear", | |
| verbose=TRUE) { | |
| if (is.null(format)) { | |
| stop("Output format has to be specified, supported formats are plink ", | |
| "snptest, gemma, limmbo and bimbam") | |
| } | |
| if (is.null(genotypes)) { | |
| vmessage(c("No genotypes provided. Remaining data still saved in ", | |
| paste(format, collapse=","), " format."), verbose=verbose) | |
| } | |
| if (grepl("~", directory)) { | |
| stop("directory contains ~: path expansion not guaranteed on | |
| every platform (see path.expand{base}), please provide full file | |
| path to the directory") | |
| } | |
| if (!dir.exists(directory)) dir.create(directory, recursive=TRUE) | |
| if ("plink" %in% format) { | |
| if (!is.null(phenotypes)) { | |
| vmessage(c("Save phenotypes in PLINK format"), verbose=verbose) | |
| if (is.null(standardInput_samples)) { | |
| pheno_format <- cbind(id_samples, id_samples, phenotypes) | |
| } else { | |
| pheno_format <- cbind(standardInput_samples[,1:2], phenotypes) | |
| } | |
| write.table(pheno_format, paste(directory, "/Ysim", outstring, | |
| "_plink.txt", sep=""), | |
| sep="\t", quote=FALSE, col.names=FALSE, row.names=FALSE) | |
| if (!is.null(additionalPhenotypes)) { | |
| vmessage(c("Save additional phenotypes in PLINK format"), | |
| verbose=verbose) | |
| if (is.null(standardInput_samples)) { | |
| pheno_format <- cbind(id_samples, id_samples, | |
| additionalPhenotypes) | |
| } else { | |
| pheno_format <- cbind(standardInput_samples[,1:2], | |
| additionalPhenotypes) | |
| } | |
| write.table(pheno_format, paste(directory, "/Ysim", | |
| nameAdditional, outstring, | |
| "_plink.txt", sep=""), | |
| sep="\t", quote=FALSE, col.names=FALSE, | |
| row.names=FALSE) | |
| } | |
| } | |
| if (!is.null(genotypes)) { | |
| vmessage(c("Save genotypes in PLINK format"), verbose=verbose) | |
| if (is.null(standardInput_genotypes)) { | |
| N <- nrow(genotypes) | |
| X_id <- data.frame(FID=id_samples, IID=id_samples, | |
| PAT=rep(0, N), MAT=rep(0, N), SEX=rep(0, N), | |
| PHENOTYPE=rep(-9, N)) | |
| rownames(X_id) <- id_samples | |
| } else { | |
| X_id <- standardInput_genotypes | |
| colnames(X_id) <- c("FID", "IID", "PAT", "MAT", "SEX", | |
| "PHENOTYPE") | |
| } | |
| plink.out <- snpStats::write.plink(file.base=paste(directory, | |
| "/Genotypes", | |
| outstring, | |
| sep=""), | |
| snps=as(genotypes, "SnpMatrix"), | |
| sex=X_id$SEX, | |
| father=X_id$PAT, | |
| mother=X_id$MAT, | |
| pedigree=X_id$FID, | |
| id=X_id$IID, | |
| phenotype=X_id$PHENOTYPE) | |
| } | |
| if (!is.null(covariates)) { | |
| vmessage(c("Save covariates in PLINK format"), verbose=verbose) | |
| if (is.null(standardInput_samples)) { | |
| covs_format <- cbind(id_samples, id_samples, covariates) | |
| } else { | |
| covs_format <- cbind(standardInput_samples[,1:2], covariates) | |
| } | |
| colnames(covs_format) <- c("FID", "IID", colnames(covariates)) | |
| write.table(covs_format, paste(directory, "/Covs", outstring, | |
| "_plink.txt", sep=""), | |
| sep="\t", quote=FALSE, col.names=TRUE, row.names=FALSE) | |
| } | |
| if (!is.null(kinship)) { | |
| vmessage(c("PLINK format does not support a kinship, supplied ", | |
| "kinship ignored"), verbose=verbose) | |
| } | |
| } | |
| if ("bimbam" %in% format) { | |
| if (!is.null(phenotypes)) { | |
| vmessage(c("Save phenotypes in BIMBAM format"), verbose=verbose) | |
| write.table(phenotypes, | |
| paste(directory, "/Ysim", outstring, "_bimbam.txt", | |
| sep=""), | |
| sep="\t", quote=FALSE, col.names=FALSE, row.names=FALSE) | |
| if (!is.null(additionalPhenotypes)) { | |
| vmessage(c("Save additional phenotypes in BIMBAM format"), | |
| verbose=verbose) | |
| write.table(additionalPhenotypes, | |
| paste(directory, "/Ysim", nameAdditional, outstring, | |
| "_bimbam.txt", | |
| sep=""), | |
| sep="\t", quote=FALSE, col.names=FALSE, | |
| row.names=FALSE) | |
| } | |
| } | |
| if (!is.null(genotypes)) { | |
| vmessage(c("Save genotypes in BIMBAM format"), verbose=verbose) | |
| if (is.null(standardInput_genotypes)) { | |
| geno_format <- cbind(id_snps, rep("A", length(id_snps)), | |
| rep("B", length(id_snps)), t(genotypes)) | |
| } else { | |
| geno_format <- standardInput_genotypes | |
| } | |
| write.table(geno_format, | |
| paste(directory, "/Genotypes", outstring, "_bimbam.csv", | |
| sep=""), | |
| sep=",", col.names=FALSE, row.names=FALSE, quote=FALSE) | |
| } | |
| if (!is.null(covariates)) { | |
| vmessage(c("BIMBAM format does not support covariates, supplied ", | |
| "covariates ignored"), verbose=verbose) | |
| } | |
| if (!is.null(kinship)) { | |
| vmessage(c("BIMBAM format does not support a kinship, supplied ", | |
| "kinship ignored"), verbose=verbose) | |
| } | |
| } | |
| if ("gemma" %in% format) { | |
| if (!is.null(phenotypes)) { | |
| vmessage(c("Save phenotypes in GEMMA format"), verbose=verbose) | |
| write.table(phenotypes, | |
| paste(directory, "/Ysim", outstring, "_gemma.txt", | |
| sep=""), | |
| sep="\t", quote=FALSE, col.names=FALSE, row.names=FALSE) | |
| if (!is.null(additionalPhenotypes)) { | |
| vmessage(c("Save additional phenotypes in GEMMA format"), | |
| verbose=verbose) | |
| write.table(additionalPhenotypes, | |
| paste(directory, "/Ysim", nameAdditional, outstring, | |
| "_gemma.txt", | |
| sep=""), | |
| sep="\t", quote=FALSE, col.names=FALSE, | |
| row.names=FALSE) | |
| } | |
| } | |
| if (!is.null(genotypes)) { | |
| vmessage(c("Save genotypes in GEMMA format"), verbose=verbose) | |
| if (is.null(standardInput_genotypes)) { | |
| geno_format <- cbind(id_snps, rep("A", length(id_snps)), | |
| rep("B", length(id_snps)), t(genotypes)) | |
| } else { | |
| geno_format <- standardInput_genotypes | |
| } | |
| write.table(geno_format, | |
| paste(directory, "/Genotypes", outstring, "_gemma.txt", | |
| sep=""), | |
| sep=",", col.names=FALSE, row.names=FALSE, quote=FALSE) | |
| } | |
| if (!is.null(kinship)) { | |
| vmessage(c("Save kinship in GEMMA format"), verbose=verbose) | |
| write.table(kinship, | |
| paste(directory, "/Kinship", outstring, "_gemma.txt", | |
| sep=""), | |
| sep="\t", quote=FALSE, col.names=FALSE, row.names=FALSE) | |
| write.table(evec_kinship, paste(directory, | |
| "/Kinship_eigenvec_gemma.txt", | |
| sep=""), | |
| sep=" ", quote=FALSE, col.names=FALSE, row.names=FALSE) | |
| write.table(eval_kinship, paste(directory, | |
| "/Kinship_eigenval_gemma.txt", | |
| sep=""), | |
| sep=" ", quote=FALSE, col.names=FALSE, row.names=FALSE) | |
| } | |
| if (!is.null(covariates)) { | |
| vmessage(c("Save covariates in GEMMA format"), verbose=verbose) | |
| if (intercept_gemma) { | |
| covariates <- cbind(rep(1, length(id_samples)), covariates) | |
| } | |
| write.table(covariates, | |
| paste(directory, "/Covs", outstring, "_gemma.txt", | |
| sep=""), | |
| sep="\t", quote=FALSE, col.names=FALSE, row.names=FALSE) | |
| } | |
| } | |
| if ("limmbo" %in% format) { | |
| if (!is.null(phenotypes)) { | |
| vmessage(c("Save phenotypes in LiMMBo format"), verbose=verbose) | |
| write.table(phenotypes, | |
| paste(directory, "/Ysim", outstring, "_limmbo.csv", | |
| sep=""), | |
| sep=",", quote=FALSE, col.names=NA, row.names=TRUE) | |
| if (!is.null(additionalPhenotypes)) { | |
| vmessage(c("Save additional phenotypes in LiMMBo format"), | |
| verbose=verbose) | |
| write.table(additionalPhenotypes, | |
| paste(directory, "/Ysim", nameAdditional, outstring, | |
| "_limmbo.csv", | |
| sep=""), | |
| sep=",", quote=FALSE, col.names=NA, row.names=TRUE) | |
| } | |
| } | |
| if (!is.null(genotypes)) { | |
| vmessage(c("Save genotypes in LiMMBo format"), verbose=verbose) | |
| geno_format <- cbind(id_snps, t(genotypes)) | |
| write.table(geno_format, | |
| paste(directory, "/Genotypes", outstring, "_limmbo.csv", | |
| sep=""), | |
| sep=",", col.names=TRUE, row.names=FALSE, quote=FALSE) | |
| } | |
| if (!is.null(kinship)) { | |
| vmessage(c("Save kinship in LiMMBo format"), verbose=verbose) | |
| write.table(kinship, | |
| paste(directory, "/Kinship", outstring, "_limmbo.csv", | |
| sep=""), | |
| sep=",", quote=FALSE, col.names=TRUE, row.names=FALSE) | |
| write.table(evec_kinship, paste(directory, | |
| "/Kinship_eigenvec_limmbo.csv", | |
| sep=""), | |
| sep=",", quote=FALSE, col.names=colnames(kinship), | |
| row.names=FALSE) | |
| write.table(eval_kinship, paste(directory, | |
| "/Kinship_eigenval_limmbo.csv", | |
| sep=""), | |
| sep=",", quote=FALSE, col.names=FALSE, row.names=FALSE) | |
| } | |
| if (!is.null(covariates)) { | |
| vmessage(c("Save covariates in LiMMBo format"), verbose=verbose) | |
| write.table(covariates, | |
| paste(directory, "/Covs", outstring, "_limmbo.csv", | |
| sep=""), | |
| sep=",", quote=FALSE, col.names=NA, row.names=TRUE) | |
| } | |
| } | |
| if ("snptest" %in% format) { | |
| if (!is.null(phenotypes)) { | |
| line2 <- rep("P", length(id_phenos)) | |
| pheno_tmp <- rbind(line2, phenotypes) | |
| if (is.null(standardInput_samples)) { | |
| line2 <- c(0, 0, 0) | |
| samples_tmp <- cbind(ID_1=id_samples, | |
| ID_2=id_samples, | |
| missing=rep(0, length(id_samples))) | |
| samples_tmp <- rbind(line2 , samples_tmp) | |
| pheno_format <- cbind(samples_tmp, pheno_tmp) | |
| } else { | |
| pheno_format <- cbind(standardInput_samples[,1:3], pheno_tmp) | |
| } | |
| rownames(pheno_format) <- 1:(length(id_samples) + 1) | |
| if (is.null(covariates)) { | |
| vmessage(c("Save phenotypes in SNPTEST format"), | |
| verbose=verbose) | |
| write.table(pheno_format, | |
| paste(directory, "/Ysim", outstring, | |
| "_snptest.sample", sep=""), | |
| sep=" ", quote=FALSE, col.names=TRUE, | |
| row.names=FALSE) | |
| } | |
| if (!is.null(additionalPhenotypes)) { | |
| line2 <- rep("P", length(id_phenos)) | |
| additional_pheno_tmp <- rbind(line2, additionalPhenotypes) | |
| if (is.null(standardInput_samples)) { | |
| line2 <- c(0, 0, 0) | |
| samples_tmp <- cbind(ID_1=id_samples, | |
| ID_2=id_samples, | |
| missing=rep(0, length(id_samples))) | |
| samples_tmp <- rbind(line2 , samples_tmp) | |
| additional_pheno_format <- cbind(samples_tmp, | |
| additional_pheno_tmp) | |
| } else { | |
| additional_pheno_format <- | |
| cbind(standardInput_samples[,1:3], additional_pheno_tmp) | |
| } | |
| rownames(pheno_format) <- 1:(length(id_samples) + 1) | |
| if (is.null(covariates)) { | |
| vmessage(c("Save additional phenotypes in SNPTEST format"), | |
| verbose=verbose) | |
| write.table(additional_pheno_format, | |
| paste(directory, "/Ysim", nameAdditional, | |
| outstring, "_snptest.sample", sep=""), | |
| sep=" ", quote=FALSE, col.names=TRUE, | |
| row.names=FALSE) | |
| } | |
| } | |
| } | |
| if (!is.null(genotypes)) { | |
| vmessage(c("Save genotypes in SNPTEST format"), verbose=verbose) | |
| if (is.null(standardInput_genotypes)) { | |
| probGen <- t(apply(genotypes, 2, expGen2probGen)) | |
| geno_format <- cbind(id_snps, id_snps, 1:length(id_snps), | |
| rep("A", length(id_snps)), | |
| rep("B", length(id_snps)), probGen) | |
| } else { | |
| geno_format <- standardInput_genotypes | |
| } | |
| write.table(geno_format, | |
| paste(directory, "/Genotypes", outstring, | |
| "_snptest.gen", sep=""), | |
| col.names=FALSE, row.names=FALSE, quote=FALSE) | |
| } | |
| if (!is.null(covariates) && !is.null(phenotypes)) { | |
| vmessage(c("Save phenotypes and covariates in SNPTEST format"), | |
| verbose=verbose) | |
| line2 <- rep("C", length(colnames(covariates))) | |
| line2[grepl("cat",colnames(covariates))] <- "D" | |
| line2[grepl("bin",colnames(covariates))] <- "D" | |
| covs <- rbind(line2, covariates, make.row.names=FALSE) | |
| ids <- pheno_format[, 1:3] | |
| pheno <- pheno_format[, -c(1:3)] | |
| covs_format <- cbind(ids, covs, pheno) | |
| write.table(covs_format, | |
| paste(directory, "/Ysim", outstring, "_snptest.sample", | |
| sep=""), | |
| sep=" ", col.names=TRUE, row.names=FALSE, quote=FALSE) | |
| if (!is.null(additionalPhenotypes)) { | |
| additional_pheno <- additional_pheno_format[, -c(1:3)] | |
| covs_format <- cbind(ids, covs, additional_pheno) | |
| write.table(covs_format, | |
| paste(directory, "/Ysim", nameAdditional, | |
| outstring, "_snptest.sample", | |
| sep=""), | |
| sep=" ", col.names=TRUE, row.names=FALSE, | |
| quote=FALSE) | |
| } | |
| } | |
| if (!is.null(kinship)) { | |
| vmessage(c("SNPTEST format does not support a kinship, supplied ", | |
| "kinship ignored"), verbose=verbose) | |
| } | |
| } | |
| } | |
| #' Save final phenotype and phenotype components. | |
| #' | |
| #' savePheno saves simulated phenotypes and their components, model setup | |
| #' parameters and variance components to the specified directories. Requires a | |
| #' simulatedData list which is the output of \link{runSimulation}. | |
| #' | |
| #' @param simulatedData Named list of i) dataframe of proportion of variance | |
| #' explained for each component (varComponents), | |
| #' ii) a named list with the final simulated phenotype components | |
| #' (phenoComponentsFinal), iii) a named list with the intermediate simulated | |
| #' phenotype components (phenoComponentsIntermediate), iv) a named list of | |
| #' parameters describing the model setup (setup) and v) a named list of raw | |
| #' components (rawComponents) used for genetic effect simulation (genotypes | |
| #' and/or kinship); obtained from \link{runSimulation} | |
| #' @param directory Absolute path (no tilde expansion) to parent directory | |
| #' [string] where simulated data should be saved [needs user writing | |
| #' permission] | |
| #' @param outstring Optional name [string] of subdirectory (in relation to | |
| #' directory) to save set-up dependent simulation results; if | |
| #' set to NULL, subdirectory named by NrSamples, NrSNPs, genetic Model and | |
| #' noise Model and genVar is created. | |
| #' @param intercept_gemma [boolean] When modeling an intercept term in gemma, a | |
| #' column of 1's have to be appended to the covariate files. Set intercept_gemma | |
| #' to TRUE to include a column of 1's in the output; only used when | |
| #' "gemma" \%in\% format | |
| #' @param format Vector of format name(s) [string] specifying the output format; | |
| #' multiple output formats can be requested. Options are: plink, bimbam, | |
| #' snptest, gemma, limmbo, csv or rds. For information on format see details. In | |
| #' orde to save intermediate phenotype components, at least one of csv or rds | |
| #' need to be specified. plink/bimbam/snptest will only save final | |
| #' phenotype/genotype, kinship and covariate data. | |
| #' @param saveIntermediate [bool] If TRUE, intermediate phenotype components | |
| #' such as shared and independent effect components are saved. | |
| #' @param verbose [boolean]; If TRUE, progress info is printed to standard out | |
| #' @return Path [string] to final output directory. If outstring is | |
| #' NULL, this directory will be a subdirectory of the input directory. | |
| #' @export | |
| #' @examples | |
| #' simulatedPhenotype <- runSimulation(N=100, P=5, cNrSNP=10, | |
| #' genVar=0.2, h2s=0.2, phi=1) | |
| #' \dontrun{ | |
| #' outputdir <- savePheno(simulatedPhenotype, directory=tempdir(), | |
| #' outstring="Data_simulation", format=c("csv", "plink"))} | |
| savePheno <- function(simulatedData, directory, format=".csv", | |
| outstring="", saveIntermediate=TRUE, | |
| intercept_gemma = TRUE, verbose=TRUE) { | |
| if (grepl("~", directory)) { | |
| stop("directory contains ~: path expansion not guaranteed on | |
| every platform (see path.expand{base}), please provide full file | |
| path to the directory") | |
| } | |
| modelGenetic <- simulatedData$setup$modelGenetic | |
| modelNoise <- simulatedData$setup$modelNoise | |
| nrsamples <- simulatedData$setup$N | |
| nrpheno <- simulatedData$setup$P | |
| id_samples <- simulatedData$setup$id_samples | |
| id_phenos <- simulatedData$setup$id_phenos | |
| id_snps <- simulatedData$setup$id_snps | |
| NrSNP <- simulatedData$setup$NrCausalSNPs | |
| genVar <- simulatedData$varComponents$genVar | |
| rawComponents <- simulatedData$rawComponents | |
| phenoComponents <- simulatedData$phenoComponentsFinal | |
| phenoIntermediate <- simulatedData$phenoComponentsIntermediate | |
| ### set-up directories | |
| if (is.null(outstring)) { | |
| outstring=paste("samples", nrsamples, "_NrSNP", NrSNP, "_Cg", genVar, | |
| "_model", modelNoise, modelGenetic, sep="") | |
| } | |
| directory <- file.path(directory, outstring) | |
| if (!dir.exists(directory)) dir.create(directory, recursive=TRUE) | |
| vmessage(c("Save simulation results"), verbose=verbose) | |
| vmessage(c("Save phenotype to ", directory, "Y..."), verbose=verbose, | |
| sep="") | |
| if (outstring != "") { | |
| outstring <- paste("_", outstring, sep="") | |
| } | |
| if ("rds" %in% format) { | |
| saveRDS(phenoComponents$Y, | |
| paste(directory, "/Ysim", outstring ,".rds", sep="")) | |
| if (!is.null(phenoComponents$Y_nonLinear)) { | |
| saveRDS(phenoComponents$Y_nonLinear, | |
| paste(directory, "/Ysim_nonLinear", outstring ,".rds", | |
| sep="")) | |
| } | |
| } | |
| if ("csv" %in% format) { | |
| write.table(phenoComponents$Y, | |
| paste(directory, "/Ysim", outstring, ".csv", sep=""), | |
| sep=",", quote=FALSE, col.names=NA, row.names=TRUE) | |
| if (!is.null(phenoComponents$Y_nonLinear)) { | |
| write.table(phenoComponents$Y_nonLinear, | |
| paste(directory, "/Ysim_nonLinear", outstring, ".csv", | |
| sep=""), | |
| sep=",", quote=FALSE, col.names=NA, row.names=TRUE) | |
| } | |
| } | |
| if (grepl("Bg", modelGenetic)) { | |
| vmessage(c("Save infinitesimal genetic component to ", directory, | |
| "Y_genBg..."), verbose=verbose, sep="") | |
| if ("rds" %in% format) { | |
| saveRDS(phenoComponents$Y_genBg, | |
| paste(directory, "/Y_genBg", outstring,".rds",sep="")) | |
| saveRDS(phenoComponents$cov_genBg, | |
| paste(directory, "/cov_genBg", outstring,".rds", | |
| sep="")) | |
| if (saveIntermediate){ | |
| saveRDS(phenoIntermediate$Y_genBg_shared, | |
| paste(directory, "/Y_genBg_shared", outstring, ".rds", | |
| sep="")) | |
| saveRDS(phenoIntermediate$cov_genBg_shared, | |
| paste(directory, "/cov_genBg_shared", outstring, ".rds", | |
| sep="")) | |
| saveRDS(phenoIntermediate$Y_genBg_independent, | |
| paste(directory, "/Y_genBg_independent", outstring, | |
| ".rds", sep="")) | |
| saveRDS(phenoIntermediate$cov_genBg_independent, | |
| paste(directory, "/cov_genBg_independent", outstring, | |
| ".rds", sep="")) | |
| } | |
| } | |
| if ("csv" %in% format) { | |
| write.table(phenoComponents$Y_genBg, | |
| paste(directory, "/Y_genBg", outstring,".csv", | |
| sep=""), | |
| sep=",",quote=FALSE, col.names=NA, row.names=TRUE) | |
| write.table(phenoComponents$cov_Y_genBg, | |
| paste(directory, "/cov_genBg", outstring,".csv", | |
| sep=""), | |
| sep=",", quote=FALSE, col.names=FALSE, row.names=FALSE) | |
| if (saveIntermediate){ | |
| write.table(phenoIntermediate$Y_genBg_shared, | |
| paste(directory, "/Y_genBg_shared", outstring, | |
| ".csv", sep=""), | |
| sep=",",quote=FALSE, col.names=NA, row.names=TRUE) | |
| write.table(phenoIntermediate$cov_genBg_shared, | |
| paste(directory, "/cov_genBg_shared", outstring, | |
| ".csv", sep=""), | |
| sep=",", quote=FALSE, col.names=FALSE, | |
| row.names=FALSE) | |
| write.table(phenoIntermediate$Y_genBg_independent, | |
| paste(directory, "/Y_genBg_independent", outstring, | |
| ".csv", sep=""), | |
| sep=",",quote=FALSE, col.names=NA, row.names=TRUE) | |
| write.table(phenoIntermediate$cov_genBg_independent, | |
| paste(directory, "/cov_genBg_independent", | |
| outstring,".csv", sep=""), | |
| sep=",", quote=FALSE, col.names=FALSE, | |
| row.names=FALSE) | |
| } | |
| } | |
| vmessage(c("Save kinship to", directory), verbose=verbose) | |
| if ("rds" %in% format) { | |
| saveRDS(rawComponents$kinship, | |
| paste(directory, "/Kinship", outstring,".rds", sep="")) | |
| saveRDS(rawComponents$evec_kinship, paste(directory, | |
| "/Kinship_eigenvec", outstring, | |
| ".rds", sep="")) | |
| saveRDS(rawComponents$eval_kinship, paste(directory, | |
| "/Kinship_eigenval", outstring, | |
| ".rds", sep="")) | |
| } | |
| if ("csv" %in% format) { | |
| write.table(rawComponents$kinship, | |
| paste(directory, "/Kinship",outstring,".csv", | |
| sep=""), | |
| sep=",", col.names=TRUE, row.names=FALSE) | |
| colnames(rawComponents$evec_kinship) <- | |
| colnames(rawComponents$kinship) | |
| write.table(rawComponents$evec_kinship, paste(directory, | |
| "/Kinship_eigenvec", outstring, | |
| ".csv", sep=""), | |
| sep=",", quote=FALSE, | |
| col.names=TRUE, | |
| row.names=FALSE) | |
| write.table(rawComponents$eval_kinship, paste(directory, | |
| "/Kinship_eigenval", outstring, | |
| ".csv", sep=""), | |
| sep=",", quote=FALSE, col.names=FALSE, row.names=FALSE) | |
| } | |
| } | |
| if (grepl("Fixed", modelGenetic)) { | |
| vmessage(c("Save genetic variant effects to ", directory, | |
| "Y_genFixed..."), verbose=verbose, sep="") | |
| if ("rds" %in% format) { | |
| saveRDS(phenoComponents$Y_genFixed, | |
| paste(directory, "/Y_genFixed", outstring, ".rds", | |
| sep="")) | |
| if (saveIntermediate){ | |
| saveRDS(phenoIntermediate$Y_genFixed_shared, | |
| paste(directory, "/Y_genFixed_shared", outstring, | |
| ".rds", sep="")) | |
| saveRDS(phenoIntermediate$Y_genFixed_independent, | |
| paste(directory, "/Y_genFixed_independent", outstring, | |
| ".rds", sep="")) | |
| } | |
| } | |
| if ("csv" %in% format) { | |
| write.table(phenoComponents$Y_genFixed, | |
| paste(directory, "/Y_genFixed", outstring, ".csv", | |
| sep=""), | |
| sep=",", quote=FALSE, col.names=NA, row.names=TRUE) | |
| if (saveIntermediate){ | |
| write.table(phenoIntermediate$Y_genFixed_shared, | |
| paste(directory, "/Y_genFixed_shared", outstring, | |
| ".csv", sep=""), | |
| sep=",", quote=FALSE, col.names=NA, row.names=TRUE) | |
| write.table(phenoIntermediate$Y_genFixed_independent, | |
| paste(directory, "/Y_genFixed_independent", | |
| outstring, ".csv", sep=""), | |
| sep=",", quote=FALSE, col.names=NA, row.names=TRUE) | |
| } | |
| } | |
| vmessage(c("Save genetic variants and their effect sizes to ", | |
| directory, "SNP..."), verbose=verbose, sep="") | |
| if ("rds" %in% format) { | |
| saveRDS(phenoIntermediate$genFixed$cov, | |
| paste(directory,"/SNP_NrSNP", NrSNP, outstring, | |
| ".rds",sep="")) | |
| saveRDS(phenoIntermediate$genFixed$cov_effect, | |
| paste(directory, "/SNP_effects_NrSNP", NrSNP, | |
| outstring, ".rds",sep="")) | |
| } | |
| if ("csv" %in% format) { | |
| write.table(phenoIntermediate$genFixed$cov, | |
| paste(directory, "/SNP_NrSNP", NrSNP, | |
| outstring, ".csv",sep=""), | |
| sep=",", col.names=NA, row.names=TRUE, quote=FALSE) | |
| write.table(phenoIntermediate$genFixed$cov_effect, | |
| paste(directory, "/SNP_effects_NrSNP", NrSNP, | |
| outstring, ".csv",sep=""), | |
| sep=",", col.names=NA, row.names=TRUE, quote=FALSE) | |
| } | |
| if (outstring == "") { | |
| outstringGenFixed <- "_genFixed" | |
| } else { | |
| outstringGenFixed <- paste("_genFixed", outstring, sep="") | |
| } | |
| if ("plink" %in% format) { | |
| writeStandardOutput(directory=directory, | |
| genotypes=phenoIntermediate$genFixed$cov, | |
| outstring=outstringGenFixed, | |
| format="plink", | |
| standardInput_samples = | |
| rawComponents$genotypes$format_files$plink_fam, | |
| id_samples=id_samples, | |
| id_snps= | |
| colnames(phenoIntermediate$genFixed$cov), | |
| verbose=FALSE) | |
| } | |
| if ("gemma" %in% format) { | |
| writeStandardOutput(directory=directory, | |
| genotypes=phenoIntermediate$genFixed$cov, | |
| outstring=outstringGenFixed, | |
| format="gemma", | |
| id_samples=id_samples, | |
| id_snps= | |
| colnames(phenoIntermediate$genFixed$cov), | |
| verbose=FALSE) | |
| } | |
| if ("limmbo" %in% format) { | |
| writeStandardOutput(directory=directory, | |
| genotypes=phenoIntermediate$genFixed$cov, | |
| outstring=outstringGenFixed, | |
| format="limmbo", | |
| id_samples=id_samples, | |
| id_snps= | |
| colnames(phenoIntermediate$genFixed$cov), | |
| verbose=FALSE) | |
| } | |
| if ("snptest" %in% format) { | |
| writeStandardOutput(directory=directory, | |
| genotypes=phenoIntermediate$genFixed$cov, | |
| outstring=outstringGenFixed, | |
| format="snptest", | |
| standardInput_samples = | |
| rawComponents$genotypes$format_files$snptest_samples, | |
| id_samples=id_samples, | |
| id_snps= | |
| colnames(phenoIntermediate$genFixed$cov), | |
| verbose=FALSE) | |
| } | |
| if ("bimbam" %in% format) { | |
| writeStandardOutput(directory=directory, | |
| genotypes=phenoIntermediate$genFixed$cov, | |
| outstring=outstringGenFixed, | |
| format="bimbam", | |
| id_samples=id_samples, | |
| id_snps= | |
| colnames(phenoIntermediate$genFixed$cov), | |
| verbose=FALSE) | |
| } | |
| } | |
| if (!is.null(rawComponents$genotypes)) { | |
| vmessage(c("Save genotypes to", directory), verbose=verbose) | |
| if ("csv" %in% format) { | |
| write.table(t(rawComponents$genotypes$genotypes), | |
| paste(directory, "/Genotypes", outstring, ".csv", sep=""), | |
| sep=",", col.names=NA, row.names=TRUE, quote=FALSE) | |
| } | |
| if ("rds" %in% format) { | |
| saveRDS(t(rawComponents$genotypes$genotypes), | |
| paste(directory, "/Genotypes", outstring, ".rds", | |
| sep="")) | |
| } | |
| } | |
| if (is.null(rawComponents$genotypes) && grepl("Fixed", modelGenetic)) { | |
| vmessage(c("Only causal SNPs sampled from genoFilePrefix-genoFileSuffix", | |
| "file were read into memory, so no new genotypes files are", | |
| "written"), verbose=verbose) | |
| } | |
| if (grepl("Correlated", modelNoise)) { | |
| vmessage(c("Save correlated background to ", directory, | |
| "Y_correlatedBg..."), verbose=verbose, sep="") | |
| if ("rds" %in% format) { | |
| saveRDS(phenoComponents$Y_correlatedBg, | |
| paste(directory, "/Y_correlatedBg", outstring,".rds", | |
| sep="")) | |
| saveRDS(phenoComponents$cov_correlatedBg, | |
| paste(directory, "/cov_correlatedBg", outstring,".rds", | |
| sep="")) | |
| } | |
| if ("csv" %in% format) { | |
| write.table(phenoComponents$Y_correlatedBg, | |
| paste(directory, "/Y_correlatedBg", outstring, | |
| ".csv", sep=""), | |
| sep=",", quote=FALSE, col.names=NA, row.names=TRUE) | |
| write.table(phenoComponents$cov_correlatedBg, | |
| paste(directory, "/cov_correlatedBg", outstring, | |
| ".csv", sep=""), | |
| sep=",", quote=FALSE, col.names=FALSE, row.names=FALSE) | |
| } | |
| } | |
| if (grepl("Bg", modelNoise)) { | |
| vmessage(c("Save observational noise to ", directory, "Y_noiseBg..." | |
| ), verbose=verbose, sep="") | |
| if ("rds" %in% format) { | |
| saveRDS(phenoComponents$Y_noiseBg, | |
| paste(directory, "/Y_noiseBg", outstring,".rds", | |
| sep="")) | |
| saveRDS(phenoComponents$cov_noiseBg, | |
| paste(directory, "/cov_noiseBg", outstring,".rds", | |
| sep="")) | |
| if (saveIntermediate){ | |
| saveRDS(phenoIntermediate$Y_noiseBg_shared, | |
| paste(directory, "/Y_noiseBg_shared", outstring, ".rds", | |
| sep="")) | |
| saveRDS(phenoIntermediate$cov_noiseBg_shared, | |
| paste(directory, "/cov_noiseBg_shared", outstring, | |
| ".rds", sep="")) | |
| saveRDS(phenoIntermediate$Y_noiseBg_independent, | |
| paste(directory, "/Y_noiseBg_independent", outstring, | |
| ".rds", sep="")) | |
| saveRDS(phenoIntermediate$cov_noiseBg_independent, | |
| paste(directory, "/cov_noiseBg_independent", outstring, | |
| ".rds", sep="")) | |
| } | |
| } | |
| if ("csv" %in% format) { | |
| write.table(phenoComponents$Y_noiseBg, | |
| paste(directory, "/Y_noiseBg", outstring,".csv", | |
| sep=""), sep=",", | |
| quote=FALSE, col.names=NA, row.names=TRUE) | |
| write.table(phenoComponents$cov_Y_noiseBg, | |
| paste(directory, "/cov_noiseBg", | |
| outstring,".csv", sep=""), sep=",", | |
| quote=FALSE, col.names=FALSE, row.names=FALSE) | |
| if (saveIntermediate){ | |
| write.table(phenoIntermediate$Y_noiseBg_shared, | |
| paste(directory, "/Y_noiseBg_shared", outstring, | |
| ".csv", sep=""), | |
| sep=",",quote=FALSE, col.names=NA, row.names=TRUE) | |
| write.table(phenoIntermediate$cov_noiseBg_shared, | |
| paste(directory, "/cov_noiseBg_shared", outstring, | |
| ".csv", sep=""), | |
| sep=",", quote=FALSE, col.names=FALSE, | |
| row.names=FALSE) | |
| write.table(phenoIntermediate$Y_noiseBg_independent, | |
| paste(directory, "/Y_noiseBg_independent", | |
| outstring, ".csv", sep=""), | |
| sep=",",quote=FALSE, col.names=NA, row.names=TRUE) | |
| write.table(phenoIntermediate$cov_noiseBg_independent, | |
| paste(directory, "/cov_noiseBg_independent", | |
| outstring,".csv", sep=""), | |
| sep=",", quote=FALSE, col.names=FALSE, | |
| row.names=FALSE) | |
| } | |
| } | |
| } | |
| if (grepl("Fixed", modelNoise)) { | |
| vmessage(c("Save confounder effects to ", directory, | |
| "Y_noiseFixed..."), verbose=verbose, sep="") | |
| if ("rds" %in% format) { | |
| saveRDS(phenoComponents$Y_noiseFixed, | |
| paste(directory, "/Y_noiseFixed", outstring, ".rds", | |
| sep="")) | |
| if (saveIntermediate){ | |
| saveRDS(phenoIntermediate$Y_noiseFixed_shared, | |
| paste(directory, "/Y_noiseFixed_shared", outstring, | |
| ".rds", sep="")) | |
| saveRDS(phenoIntermediate$Y_genFixed_independent, | |
| paste(directory, "/Y_noiseFixed_independent", outstring, | |
| ".rds", sep="")) | |
| } | |
| } | |
| if ("csv" %in% format) { | |
| write.table(phenoComponents$Y_noiseFixed, | |
| paste(directory, "/Y_noiseFixed", outstring, | |
| ".csv", sep=""), | |
| sep=",", quote=FALSE, col.names=NA, row.names=TRUE) | |
| if (saveIntermediate){ | |
| write.table(phenoIntermediate$Y_noiseFixed_shared, | |
| paste(directory, "/Y_noiseFixed_shared", outstring, | |
| ".csv", sep=""), | |
| sep=",", quote=FALSE, col.names=NA, row.names=TRUE) | |
| write.table(phenoIntermediate$Y_noiseFixed_independent, | |
| paste(directory, "/Y_noiseFixed_independent", | |
| outstring, ".csv", sep=""), | |
| sep=",", quote=FALSE, col.names=NA, row.names=TRUE) | |
| } | |
| } | |
| vmessage(c("Save confounders and their effect sizes to ", | |
| directory, "Covs..."), verbose=verbose, sep="") | |
| if ("rds" %in% format) { | |
| saveRDS(phenoIntermediate$noiseFixed$cov, | |
| paste(directory, "/Covs", outstring, ".rds", sep="")) | |
| saveRDS(phenoIntermediate$noiseFixed$cov_effect, | |
| paste(directory, "/Covs_effect", outstring, ".rds", | |
| sep="")) | |
| } | |
| if ("csv" %in% format) { | |
| write.table(phenoIntermediate$noiseFixed$cov, | |
| paste(directory, "/Covs", outstring, ".csv", | |
| sep=""), | |
| sep=",", quote=FALSE, col.names=NA, row.names=TRUE) | |
| write.table(phenoIntermediate$noiseFixed$cov_effect, | |
| paste(directory, "/Covs_effect", outstring,".csv", | |
| sep=""), | |
| sep=",", quote=FALSE, col.names=NA, row.names=TRUE) | |
| } | |
| } | |
| if ("rds" %in% format) { | |
| saveRDS(simulatedData$varComponents, | |
| paste(directory, "/varComponents", outstring, ".rds", | |
| sep="")) | |
| } | |
| if ("csv" %in% format) { | |
| write.table(simulatedData$varComponents, | |
| paste(directory, "/varComponents", outstring, ".csv", | |
| sep=""), | |
| sep=",", quote=FALSE, col.names=TRUE, row.names=FALSE) | |
| } | |
| if ("plink" %in% format) { | |
| plink <- writeStandardOutput(phenotypes=phenoComponents$Y, | |
| additionalPhenotypes= | |
| phenoComponents$Y_nonLinear, | |
| genotypes=rawComponents$genotypes$genotypes, | |
| covariates=phenoIntermediate$noiseFixed$cov, | |
| kinship=rawComponents$kinship, | |
| format="plink", | |
| standardInput_samples = | |
| rawComponents$genotypes$format_files$plink_fam, | |
| directory=directory, | |
| id_samples=id_samples, | |
| id_snps=id_snps, | |
| id_phenos=id_phenos) | |
| } | |
| if ("snptest" %in% format) { | |
| snptest <- writeStandardOutput(phenotypes=phenoComponents$Y, | |
| additionalPhenotypes= | |
| phenoComponents$Y_nonLinear, | |
| genotypes=rawComponents$genotypes$genotypes, | |
| covariates=phenoIntermediate$noiseFixed$cov, | |
| format="snptest", | |
| standardInput_genotypes = | |
| rawComponents$genotypes$format_files$oxgen_genotypes, | |
| standardInput_samples = | |
| rawComponents$genotypes$format_files$snptest_samples, | |
| directory=directory, | |
| id_samples=id_samples, | |
| id_snps=id_snps, | |
| id_phenos=id_phenos) | |
| } | |
| if ("bimbam" %in% format) { | |
| bimbam <- writeStandardOutput(phenotypes=phenoComponents$Y, | |
| additionalPhenotypes= | |
| phenoComponents$Y_nonLinear, | |
| genotypes=rawComponents$genotypes$genotypes, | |
| covariates=phenoIntermediate$noiseFixed$cov, | |
| format="bimbam", | |
| standardInput_genotypes = | |
| rawComponents$genotypes$format_files$bimbam_snp_info, | |
| directory=directory, | |
| id_samples=id_samples, | |
| id_snps=id_snps, | |
| id_phenos=id_phenos) | |
| } | |
| if ("gemma" %in% format) { | |
| gemma <- writeStandardOutput(phenotypes=phenoComponents$Y, | |
| additionalPhenotypes= | |
| phenoComponents$Y_nonLinear, | |
| genotypes=rawComponents$genotypes$genotypes, | |
| covariates=phenoIntermediate$noiseFixed$cov, | |
| kinship=rawComponents$kinship, | |
| eval_kinship=rawComponents$eval_kinship, | |
| evec_kinship=rawComponents$evec_kinship, | |
| format="gemma", | |
| intercept_gemma=intercept_gemma, | |
| standardInput_genotypes = | |
| rawComponents$genotypes$format_files$bimbam_snp_info, | |
| directory=directory, | |
| id_samples=id_samples, | |
| id_snps=id_snps, | |
| id_phenos=id_phenos) | |
| } | |
| if ("limmbo" %in% format) { | |
| limmbo <- writeStandardOutput(phenotypes=phenoComponents$Y, | |
| additionalPhenotypes= | |
| phenoComponents$Y_nonLinear, | |
| genotypes=rawComponents$genotypes$genotypes, | |
| covariates=phenoIntermediate$noiseFixed$cov, | |
| kinship=rawComponents$kinship, | |
| eval_kinship=rawComponents$eval_kinship, | |
| evec_kinship=rawComponents$evec_kinship, | |
| format="limmbo", | |
| directory=directory, | |
| id_samples=id_samples, | |
| id_snps=id_snps, | |
| id_phenos=id_phenos) | |
| } | |
| return(directory=directory) | |
| } |