How to keep full chromosome name when my chromosome prefix is "chr" or "Chr"?

kbroman / qtl

R/qtl: A QTL mapping environment

https://rqtl.org

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How to keep full chromosome name when my chromosome prefix is "chr" or "Chr"? #68

Closed xiekunwhy closed 5 years ago

xiekunwhy commented 5 years ago

Hi, Kbroman, I found that read.cross is always delete the chromosome prefix when it is "chr" or "Chr", for example, read.cross return 01 02 03 ... when my true chromosome name are "Chr01" "Chr02" "Chr03" .... And I want to known is there any way to fixed the chromosome name when the name prefix is "chr" or "Chr"?

Cheers, Kun.

kbroman commented 5 years ago

I think the only way would be to paste it back on afterwards.

mycross <- read.cross( .... )
names(mycross$geno) <- paste0("chr", names(mycross$geno))