### R code from vignette source 'Formats.Rnw' ### Encoding: UTF-8 ################################################### ### code chunk number 1: Formats.Rnw:170-178 ################################################### library(GWASTools) library(SNPRelate) bed.fn <- system.file("extdata", "plinkhapmap.bed.gz", package="SNPRelate") fam.fn <- system.file("extdata", "plinkhapmap.fam.gz", package="SNPRelate") bim.fn <- system.file("extdata", "plinkhapmap.bim.gz", package="SNPRelate") gdsfile <- "snps.gds" snpgdsBED2GDS(bed.fn, fam.fn, bim.fn, gdsfile, family=TRUE, cvt.chr="int", cvt.snpid="int", verbose=FALSE) ################################################### ### code chunk number 2: Formats.Rnw:188-215 ################################################### (gds <- GdsGenotypeReader(gdsfile, YchromCode=24L, XYchromCode=25L)) scanID <- getScanID(gds) family <- getVariable(gds, "sample.annot/family") father <- getVariable(gds, "sample.annot/father") mother <- getVariable(gds, "sample.annot/mother") sex <- getVariable(gds, "sample.annot/sex") sex[sex == ""] <- NA # sex must be coded as M/F/NA phenotype <- getVariable(gds, "sample.annot/phenotype") scanAnnot <- ScanAnnotationDataFrame(data.frame(scanID, father, mother, sex, phenotype, stringsAsFactors=FALSE)) snpID <- getSnpID(gds) chromosome <- getChromosome(gds) position <- getPosition(gds) alleleA <- getAlleleA(gds) alleleB <- getAlleleB(gds) rsID <- getVariable(gds, "snp.rs.id") snpAnnot <- SnpAnnotationDataFrame(data.frame(snpID, chromosome, position, rsID, alleleA, alleleB, stringsAsFactors=FALSE), YchromCode=24L, XYchromCode=25L) genoData <- GenotypeData(gds, scanAnnot=scanAnnot, snpAnnot=snpAnnot) getGenotype(genoData, snp=c(1,5), scan=c(1,5)) close(genoData) ################################################### ### code chunk number 3: Formats.Rnw:218-219 ################################################### unlink(gdsfile) ################################################### ### code chunk number 4: Formats.Rnw:228-233 ################################################### library(GWASTools) library(SNPRelate) vcffile <- system.file("extdata", "sequence.vcf", package="SNPRelate") gdsfile <- "snps.gds" snpgdsVCF2GDS(vcffile, gdsfile, verbose=FALSE) ################################################### ### code chunk number 5: Formats.Rnw:240-260 ################################################### (gds <- GdsGenotypeReader(gdsfile)) getScanID(gds) snpID <- getSnpID(gds) chromosome <- as.integer(getChromosome(gds)) position <- getPosition(gds) alleleA <- getAlleleA(gds) alleleB <- getAlleleB(gds) rsID <- getVariable(gds, "snp.rs.id") qual <- getVariable(gds, "snp.annot/qual") filter <- getVariable(gds, "snp.annot/filter") snpAnnot <- SnpAnnotationDataFrame(data.frame(snpID, chromosome, position, rsID, alleleA, alleleB, qual, filter, stringsAsFactors=FALSE)) genoData <- GenotypeData(gds, snpAnnot=snpAnnot) getGenotype(genoData) close(genoData) ################################################### ### code chunk number 6: Formats.Rnw:263-264 ################################################### unlink(gdsfile)