Question: R:how to read bed file with identical Famliy ID by read.plink
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gravatar for zwang10
4.2 years ago by
zwang1010
United States
zwang1010 wrote:

I have three files, chr_22.bed,chr_22.bim,chr_22.fam. I always use read.plink from MultiPhen to get snp matrix in R

genotype=read.plink(root="/home/chr_22")

But today when I use the same command to get snp matrix, I got following error:

Error in `row.names<-.data.frame`(`*tmp*`, value = value[[1L]]) : 
  duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique value when setting 'row.names': ‘UK10K’

Then, I check the chr_22.fam file, and I found the all elements in the first column are same UK10K. The following is the first 5 row of chr_22.fam

UK10K ALS5085249 0 0 0 -9
UK10K ALS5085250 0 0 0 -9
UK10K ALS5085251 0 0 0 -9
UK10K ALS5085252 0 0 0 -9
UK10K ALS5085253 0 0 0 -9

Can someone help me here?

bed file plink R • 1.9k views
ADD COMMENTlink modified 3.4 years ago by ingrid.szilagyi0 • written 4.2 years ago by zwang1010
1

Read the fam file, and paste 1:n to FID column, write it out as new updated fam. Then use read.plink.

ADD REPLYlink written 3.4 years ago by zx87549.6k

Did you manage to solve this issue? I am also using MultiPhen and I would be interested in how you solved this. Maybe you made a new .fam file and updated the ids using plink?

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by ingrid.szilagyi0
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