Converting to GDS format

Question

[ebrown1955]

I'm trying to create nice looking LRR and BAF plots for some SNP array data that I have. I was hoping to achieve plots that also include a chromosomal ideogram. I was able to find "GWASTools" in R, however this requires my data to be in GDF format (genome data format). I have not been able to find how to create one of these files, or convert an illumina report or similar to it.

Can anyone share any expertise? Perhaps there are other tools in R that can work with a more palatable format that can also provide an ideogram plot.

Any help much appreciated!

Answer 1

[ebrown1955]

Looks like I figured it out! From the GWASTools manual:

gdsfile <- tempfile()
path <- system.file("extdata", "illumina_raw_data", package="GWASdata")
data(illumina_snp_annot, illumina_scan_annot)
snpAnnot <- illumina_snp_annot[,c("snpID", "rsID", "chromosome","position", "alleleA", "alleleB")]
names(snpAnnot)[2] <- "snpName"
# subset of samples for testing
scanAnnot <- illumina_scan_annot[1:3, c("scanID", "genoRunID", "file")]
names(scanAnnot)[2] <- "scanName"
col.nums <- as.integer(c(1,2,12,13))
names(col.nums) <- c("snp", "sample", "a1", "a2")
diagfile <- tempfile()