createDataFile returns empty diag.geno.file

[ryshi06]

Hi,

I have raw text files from Illumina and I am following the DataCleaning guide to prepare the snpAnnotation and scanAnnotation data frame. But when I tried to generate the gds file, the corresponding diagnostic file returns NULL for several values including sample, sample.match, etc. I have attached the empty output I received. I double-checked the file path, the two annotation dataframe and the raw data files are good. Can you give me some idea why I am having this issue? Thank you!

[smgogarten]

I can't diagnose this problem without a reproducible example.

[smgogarten]

Can you please also supply the code you used that produced the error, and the output of sessionInfo()?

[smgogarten]

Email attachments don't seem to work in replying to GitHub issues. Please go to the Issue page on the github website and paste your code into the comment box.

[ryshi06]

Generate SnpAnnot:

ref <- read.table("GDA_A1_snps.txt", sep="\t", header = FALSE)
colnames(ref) <- c("snpName", "chromosome", "position", "perc_match", "strand", "TOP")

d1 <- subset(ref, select=c("snpName", "chromosome", "position"))

d1$chromosome[d1$chromosome=="X"] <- 23
d1$chromosome[d1$chromosome=="Y"] <- 25
d1$chromosome[d1$chromosome=="MT"] <- 26
d1$chromosome[d1$chromosome=="0"] <- 27

d1$chromosome[d1$chromosome=="XY"] <- 24

d1$chromosome <- as.integer(d1$chromosome)
d <- d1[order(d1$chromosome, d1$position), ]
d$snpID <- 1:nrow(d)
d <- d[,c("snpID", "snpName", "chromosome", "position")]
snpAnnot <- SnpAnnotationDataFrame(d)

meta <- varMetadata(snpAnnot)
meta[c("snpID", "snpName", "chromosome", "position"),
"labelDescription"] <- c("unique integer ID for SNPs (row number assigned)",
"BeadSet SNP ID from Illumina",
paste("integer code for chromosome: 1:22=autosomes,",
"23=X, 24=pseudoautosomal, 25=Y, 26=Mitochondrial, 27=Unknown"), "base pair position on chromosome (build 37)")
varMetadata(snpAnnot) <- meta

Generate ScanAnnot:
d <- read.table("scanAnnot_fake.txt", sep = "\t", header = TRUE)

scanAnnot <- ScanAnnotationDataFrame(d)

meta <- varMetadata(scanAnnot)
meta[c("scanID","scanName","file","sex","race"), "labelDescription"] <-
c("unique ID for scans",
"subject identifier",
"raw data file",
"Sex",
"Race")
varMetadata(scanAnnot) <- meta

Create gds file:
path <- "."
geno.file <- "tmp.geno.gds"

scan_annotation <- getAnnotation(scanAnnot)
snp_annotation <- getAnnotation(snpAnnot)

col.nums <- as.integer(c(1,2,10,11))
names(col.nums) <- c("snp", "sample", "a1", "a2")
diag.geno.file <- "diag.geno.RData"
diag.geno <- createDataFile(path=path, geno.file, file.type="gds",
variables="genotype",
snp.annotation=snp_annotation,
scan.annotation=scan_annotation, sep.type="\t",
skip.num=10, col.total=11, col.nums=col.nums,
scan.name.in.file=1, diagnostics.filename=diag.geno.file)

sample1.txt
sample2.txt
sample3.txt
scanAnnot_fake.txt
GDA_A1_snps.txt

[smgogarten]

I just ran your code and got the expected (non-empty) output:

> diag.geno
$read.file
[1] 1 1 1

$row.num
[1] 90 90 90

$samples
$samples[[1]]
[1] "sample1"

$samples[[2]]
[1] "sample2"

$samples[[3]]
[1] "sample3"


$sample.match
[1] 1 1 1

$missg
$missg[[1]]
character(0)

$missg[[2]]
character(0)

$missg[[3]]
character(0)


$snp.chk
[1] 1 1 1

$chk
[1] 1 1 1

Details on my R session:

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Los_Angeles
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GWASTools_1.46.0    Biobase_2.60.0      BiocGenerics_0.46.0

loaded via a namespace (and not attached):
 [1] shape_1.4.6          formula.tools_1.7.1  lattice_0.21-8       vctrs_0.6.3         
 [5] tools_4.3.1          generics_0.1.3       sandwich_3.0-2       tibble_3.2.1        
 [9] fansi_1.0.4          RSQLite_2.3.1        pan_1.9              blob_1.2.4          
[13] pkgconfig_2.0.3      jomo_2.7-6           Matrix_1.6-0         data.table_1.14.8   
[17] lifecycle_1.0.3      compiler_4.3.1       MatrixModels_0.5-2   codetools_0.2-19    
[21] SparseM_1.81         quantreg_5.97        GWASExactHW_1.01     glmnet_4.1-8        
[25] mice_3.16.0          pillar_1.9.0         nloptr_2.0.3         tidyr_1.3.0         
[29] MASS_7.3-60          cachem_1.0.8         iterators_1.0.14     rpart_4.1.19        
[33] boot_1.3-28.1        foreach_1.5.2        mitml_0.4-5          nlme_3.1-162        
[37] tidyselect_1.2.0     dplyr_1.1.2          purrr_1.0.1          splines_4.3.1       
[41] operator.tools_1.6.3 fastmap_1.1.1        grid_4.3.1           cli_3.6.1           
[45] magrittr_2.0.3       survival_3.5-5       utf8_1.2.3           broom_1.0.5         
[49] backports_1.4.1      bit64_4.0.5          quantsmooth_1.66.0   logistf_1.26.0      
[53] bit_4.0.5            nnet_7.3-19          lme4_1.1-34          zoo_1.8-12          
[57] memoise_2.0.1        DNAcopy_1.74.1       lmtest_0.9-40        mgcv_1.9-0          
[61] rlang_1.1.1          Rcpp_1.0.11          glue_1.6.2           DBI_1.1.3           
[65] gdsfmt_1.36.1        rstudioapi_0.15.0    minqa_1.2.5          R6_2.5.1 

[ryshi06]

Thank you. Let me double check my R session info and hopefully I can get the normal output. Best, Ruyu From: Stephanie M. Gogarten ***@***.***> Date: Thursday, September 21, 2023 at 6:50 PM To: smgogarten/GWASTools ***@***.***> Cc: Shi, Ruyu ***@***.***>, Author ***@***.***> Subject: Re: [smgogarten/GWASTools] createDataFile returns empty diag.geno.file (Issue #15) I just ran your code and got the expected (non-empty) output:

diag.geno

$read.file [1] 1 1 1 $row.num [1] 90 90 90 $samples $samples[[1]] [1] "sample1" $samples[[2]] [1] "sample2" $samples[[3]] [1] "sample3" $sample.match [1] 1 1 1 $missg $missg[[1]] character(0) $missg[[2]] character(0) $missg[[3]] character(0) $snp.chk [1] 1 1 1 $chk [1] 1 1 1 Details on my R session:

sessionInfo()

R version 4.3.1 (2023-06-16) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.4 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: America/Los_Angeles tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GWASTools_1.46.0 Biobase_2.60.0 BiocGenerics_0.46.0 loaded via a namespace (and not attached): [1] shape_1.4.6 formula.tools_1.7.1 lattice_0.21-8 vctrs_0.6.3 [5] tools_4.3.1 generics_0.1.3 sandwich_3.0-2 tibble_3.2.1 [9] fansi_1.0.4 RSQLite_2.3.1 pan_1.9 blob_1.2.4 [13] pkgconfig_2.0.3 jomo_2.7-6 Matrix_1.6-0 data.table_1.14.8 [17] lifecycle_1.0.3 compiler_4.3.1 MatrixModels_0.5-2 codetools_0.2-19 [21] SparseM_1.81 quantreg_5.97 GWASExactHW_1.01 glmnet_4.1-8 [25] mice_3.16.0 pillar_1.9.0 nloptr_2.0.3 tidyr_1.3.0 [29] MASS_7.3-60 cachem_1.0.8 iterators_1.0.14 rpart_4.1.19 [33] boot_1.3-28.1 foreach_1.5.2 mitml_0.4-5 nlme_3.1-162 [37] tidyselect_1.2.0 dplyr_1.1.2 purrr_1.0.1 splines_4.3.1 [41] operator.tools_1.6.3 fastmap_1.1.1 grid_4.3.1 cli_3.6.1 [45] magrittr_2.0.3 survival_3.5-5 utf8_1.2.3 broom_1.0.5 [49] backports_1.4.1 bit64_4.0.5 quantsmooth_1.66.0 logistf_1.26.0 [53] bit_4.0.5 nnet_7.3-19 lme4_1.1-34 zoo_1.8-12 [57] memoise_2.0.1 DNAcopy_1.74.1 lmtest_0.9-40 mgcv_1.9-0 [61] rlang_1.1.1 Rcpp_1.0.11 glue_1.6.2 DBI_1.1.3 [65] gdsfmt_1.36.1 rstudioapi_0.15.0 minqa_1.2.5 R6_2.5.1 — Reply to this email directly, view it on GitHub<#15 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AONEF5L7TYCPRSFGVYKPL7LX3TACFANCNFSM6AAAAAA4XIA2ME>. You are receiving this because you authored the thread.Message ID: ***@***.***>