R:how to read bed file with identical Famliy ID by read.plink
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?
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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?
Read the fam file, and paste 1:n to FID column, write it out as new updated fam. Then use read.plink.