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 |
|
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
1 2 3 4 5 6 7 8 9 10 11 | 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)
|
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