write.beagle: Prepare genotypic data for Beagle
In synbreed: Framework for the Analysis of Genomic Prediction Data using R

Description Usage Arguments Details Value Author(s) References See Also Examples

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.

1	write.beagle(gp, wdir = getwd(), prefix)

`gp`	`gpData` object with elements `geno` and `map`
`wdir`	`character`. Directory for Beagle input files
`prefix`	`character`. Prefix for Beagle input files.

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

codeGeno

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")