write.beagle {synbreed} | R Documentation |
Create input file for Beagle software (Browning and Browning 2009) from an object of class gpData
. This function is created for usage within function codeGeno
to impute missing values.
write.beagle(gp, wdir = getwd(), prefix)
gp |
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wdir |
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prefix |
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The Beagle software must be used chromosomewise. Consequently, gp
should contain only data from one chromosome (use discard.markers, see Examples
).
No value is returned. Function creates files [prefix]ingput.bgl
with genotypic data in Beagle input format and [prefix]marker.txt
with marker information used by Beagle.
Valentin Wimmer
B L Browning and S R Browning (2009) A unified approach to genotype imputation and haplotype phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet 84:210-22
map <- data.frame(chr=c(1,1,1,1,1,2,2,2,2),pos=1:9) geno <- matrix(sample(c(0,1,2,NA),size=10*9,replace=TRUE),nrow=10,ncol=9) colnames(geno) <- rownames(map) <- paste("SNP",1:9,sep="") rownames(geno) <- paste("ID",1:10+100,sep="") gp <- create.gpData(geno=geno,map=map) gp1 <- discard.markers(gp,rownames(map[map$chr!=1,])) ## Not run: write.beagle(gp1,prefix="test")