R: read.plink Error

Question

[zwang10]

Using read.plink from snpMatrix

I use following command to read bed file in R:

read.plink("/home/chr22_pos_16854001_to_16857000",na.strings = "-9")

However, it shows

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

It is weird that when I read chr22_pos_16050001_to_16053000.bed using same command, there is no such error. Can someone help me here?

I use following command from plink to get bed file

$/home/zwang10/research/plink --bfile chr22 --chr 22 --from-bp 16854001 --to-bp 16857001 --make-bed --out chr22_16854001_to_16857001
    PLINK v1.90b3.35 64-bit (25 Mar 2016)      https://www.cog-genomics.org/plink2
    (C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3
    Logging to chr22_16854001_to_16857001.log.
    Options in effect:
      --bfile chr22
      --chr 22
      --from-bp 16854001
      --make-bed
      --out chr22_16854001_to_16857001
      --to-bp 16857001

    32134 MB RAM detected; reserving 16067 MB for main workspace.
    9 variants loaded from .bim file.
    1497 people (0 males, 0 females, 1497 ambiguous) loaded from .fam.
    Ambiguous sex IDs written to chr22_16854001_to_16857001.nosex .
    Using 1 thread (no multithreaded calculations invoked).
    Before main variant filters, 1497 founders and 0 nonfounders present.
    Calculating allele frequencies... done.
    9 variants and 1497 people pass filters and QC.
    Note: No phenotypes present.
    --make-bed to chr22_16854001_to_16857001.bed + chr22_16854001_to_16857001.bim +
    chr22_16854001_to_16857001.fam ... done.

And then I use awk '{print $2}' chr22_16854001_to_16857001.fam | sort | uniq -d to check whether there are duplicated individual. But I got no output. I did find the famliy name are same, but individual name is different, part of fam file.

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
UK10K ALS5085254 0 0 0 -9
UK10K ALS5085255 0 0 0 -9
UK10K ALS5085256 0 0 0 -9
UK10K ALS5085257 0 0 0 -9
UK10K ALS5085258 0 0 0 -9

One interesting thing is when I set pos1=16050001 and pos2=16053000, and get the chr22_16050001_to_16053000.bed file. Then, I use same command to read bed file, and there is no such error.

[Floris Brenk]

It says "duplicate 'row.names' are not allowed" so maybe investigate you file for duplicate row.names?

something like cut -f 1 FILE | sort | uniq -d

[zwang10]

I did not get any output.

Answer 1

[chrchang523]

The duplicate "." IDs are in the .bim file, not the .fam file. --set-missing-var-ids provides one way to replace them with unique IDs.

[zwang10]

Thank you very much for your help.let me try.