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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,18 +1,18 @@ | ||
| Package: CrypticIBDcheck | ||
| Type: Package | ||
| Title: Identifying cryptic relatedness in genetic association studies | ||
| Version: 0.3-1 | ||
| Date: 2012-04-14 | ||
| Title: Identifying Cryptic Relatedness in Genetic Association Studies | ||
| Version: 0.3-3 | ||
| Date: 2018-05-14 | ||
| Author: Annick Joelle Nembot-Simo, Jinko Graham and Brad McNeney | ||
| Maintainer: Brad McNeney <mcneney@sfu.ca> | ||
| Depends: R (>= 2.14.0), rJPSGCS (>= 0.2-5), car (>= 2.0-9), ellipse (>= | ||
| 0.3-5) | ||
| Imports: chopsticks | ||
| Imports: chopsticks, methods | ||
| Suggests: parallel | ||
| Description: Exploratory tools to identify closely related subjects using autosomal genetic marker data. | ||
| License: GPL-3 | ||
| LazyData: yes | ||
| Packaged: 2013-09-20 21:38:23 UTC; mcneney | ||
| LazyData: true | ||
| NeedsCompilation: yes | ||
| Packaged: 2018-05-17 08:25:12 UTC; mcneney | ||
| Repository: CRAN | ||
| Date/Publication: 2013-09-21 08:05:29 | ||
| Date/Publication: 2018-05-17 09:01:55 UTC |
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|---|---|---|
| @@ -1,2 +1,12 @@ | ||
| export(countIBS,IBDcheck,new.IBD,IBD,SNPgenmap,filter.control,sim.control) | ||
| importFrom("grDevices", "devAskNewPage") | ||
| importFrom("graphics", "lines", "plot", "title") | ||
| importFrom("methods", "is", "new") | ||
| importFrom("stats", "approxfun", "cor", "pnorm", "qchisq", "quantile", | ||
| "rbinom", "sd", "var") | ||
| importFrom("utils", "flush.console") | ||
| importFrom("rJPSGCS","GeneDrops","read.pedfile","write.pedfile","write.parfile","FitGMLD") | ||
| importFrom("car","showLabels") | ||
| importFrom("ellipse","ellipse") | ||
| S3method(plot,IBD) | ||
| useDynLib("CrypticIBDcheck", .registration = TRUE) |
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,52 +1,52 @@ | ||
| ## filter.control is a function to set parameters that control quality control | ||
| ## filters: snpcallrate, MAF, samplecallrate and HWEp | ||
|
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| filter.control<-function(filter=TRUE,snpcallrate=0.9,MAF=0.01, | ||
| samplecallrate=0.9, HWEp=0.001) { | ||
| list(filter=filter,snpcallrate=snpcallrate,MAF=MAF, | ||
| samplecallrate=samplecallrate, HWEp=HWEp) | ||
| } | ||
|
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| ################################################################ | ||
| snpfilter <- function(snpmatlist1,filter){ | ||
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| SNP.support=snpmatlist1$snp.support | ||
| SNP.support=remove.cdlIBS(SNP.support) #remove cdlIBS columns, if present | ||
| snpobjt=snpmatlist1$snp.data | ||
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| sumsnp<-chopsticks::summary(snpobjt) | ||
| nbs=ncol(snpobjt) | ||
|
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| #snps call rate test | ||
| callr=(sumsnp$Call.rate>=filter$snpcallrate) | ||
| snpobjt1<-snpobjt[,(callr)] | ||
| SNP.support1<-SNP.support[callr,] | ||
|
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| #MAF test | ||
| sumsnp1<-chopsticks::summary(snpobjt1) | ||
| maft=(sumsnp1$MAF>=filter$MAF) | ||
| snpobjt1<-snpobjt1[,(maft)] | ||
| SNP.support1<-SNP.support1[maft,] | ||
|
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| #samples call rate test | ||
| callrvt=(row.summary(snpobjt1)$Call.rate>=filter$samplecallrate) | ||
| snpobjt1<-snpobjt1[(callrvt),] | ||
| snpmatlist1$subject.support<-snpmatlist1$subject.support[(callrvt),] | ||
|
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| #Remove SNPs not found by SNPgenmap (NA genetic location) | ||
| ind<-is.na(SNP.support1$Gen_loc) | ||
| SNP.support1<-SNP.support1[!ind,] | ||
| snpobjt1<-snpobjt1[,(!ind)] | ||
|
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| #Do test of HWE and keep SNPs that pass | ||
| vecpval=as.numeric(as.vector(SNP.support1$pvalue_HWE)) | ||
| hwvec<-( vecpval>filter$HWEp & !is.na(SNP.support1$pvalue_HWE) ) | ||
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| snpmatlist1$snp.data<-snpobjt1[,(hwvec)] | ||
| snpmatlist1$snp.support<-SNP.support1[hwvec,] | ||
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| return(snpmatlist1) | ||
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| } | ||
|
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| ## filter.control is a function to set parameters that control quality control | ||
| ## filters: snpcallrate, MAF, samplecallrate and HWEp | ||
|
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| filter.control<-function(filter=TRUE,snpcallrate=0.9,MAF=0.01, | ||
| samplecallrate=0.9, HWEp=0.001) { | ||
| list(filter=filter,snpcallrate=snpcallrate,MAF=MAF, | ||
| samplecallrate=samplecallrate, HWEp=HWEp) | ||
| } | ||
|
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| ################################################################ | ||
| snpfilter <- function(snpmatlist1,filter){ | ||
|
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| SNP.support=snpmatlist1$snp.support | ||
| SNP.support=remove.cdlIBS(SNP.support) #remove cdlIBS columns, if present | ||
| snpobjt=snpmatlist1$snp.data | ||
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| sumsnp<-chopsticks::summary(snpobjt) | ||
| nbs=ncol(snpobjt) | ||
|
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| #snps call rate test | ||
| callr=(sumsnp$Call.rate>=filter$snpcallrate) | ||
| snpobjt1<-snpobjt[,(callr)] | ||
| SNP.support1<-SNP.support[callr,] | ||
|
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| #MAF test | ||
| sumsnp1<-chopsticks::summary(snpobjt1) | ||
| maft=(sumsnp1$MAF>=filter$MAF) | ||
| snpobjt1<-snpobjt1[,(maft)] | ||
| SNP.support1<-SNP.support1[maft,] | ||
|
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| #samples call rate test | ||
| callrvt=(chopsticks::row.summary(snpobjt1)$Call.rate>=filter$samplecallrate) | ||
| snpobjt1<-snpobjt1[(callrvt),] | ||
| snpmatlist1$subject.support<-snpmatlist1$subject.support[(callrvt),] | ||
|
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| #Remove SNPs not found by SNPgenmap (NA genetic location) | ||
| ind<-is.na(SNP.support1$Gen_loc) | ||
| SNP.support1<-SNP.support1[!ind,] | ||
| snpobjt1<-snpobjt1[,(!ind)] | ||
|
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| #Do test of HWE and keep SNPs that pass | ||
| vecpval=as.numeric(as.vector(SNP.support1$pvalue_HWE)) | ||
| hwvec<-( vecpval>filter$HWEp & !is.na(SNP.support1$pvalue_HWE) ) | ||
|
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| snpmatlist1$snp.data<-snpobjt1[,(hwvec)] | ||
| snpmatlist1$snp.support<-SNP.support1[hwvec,] | ||
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| return(snpmatlist1) | ||
|
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| } | ||
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