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 |
|
wdir |
|
prefix |
|
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") ## End(Not run)