I am wondering if anyone has encountered this issue when using locuszoom in species other than human.
I am working with cattle which has 29 autosomes and have created my own database for it.
I also modified the chr2chrom and chrom2chr fuction in locuszoom r script to allow plot correctly for 29 autosomes.
Codes:
chrom2chr <- function (x) {
y <- substring(x,first=4);
as.numeric(y);
}
chr2chrom <- function (x) {
return (paste("chr",as.numeric(x),sep=""));
}
Still, I can only get the correct information from refFlat up to chr22.
For the rest of the autosomes, it did not work. When I checked the temporary files, my refFlatRaw and refFlat_in_the_region were empty. However, arg[[chr]] was correct.
I have checked that my database does contain information for all the chromosomes.
Does anyone know where else in the script that I need to modify to make it work?
Dear all,
I am wondering if anyone has encountered this issue when using locuszoom in species other than human.
I am working with cattle which has 29 autosomes and have created my own database for it. I also modified the chr2chrom and chrom2chr fuction in locuszoom r script to allow plot correctly for 29 autosomes. Codes:
chrom2chr <- function (x) { y <- substring(x,first=4); as.numeric(y); }
chr2chrom <- function (x) { return (paste("chr",as.numeric(x),sep="")); }
Still, I can only get the correct information from refFlat up to chr22. For the rest of the autosomes, it did not work. When I checked the temporary files, my refFlatRaw and refFlat_in_the_region were empty. However, arg[[chr]] was correct. I have checked that my database does contain information for all the chromosomes.
Does anyone know where else in the script that I need to modify to make it work?
I appreciate any input.
Best wishes, Zih-Hua