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I have a .txt file; I have 139 unique sample IDs in sampleID column

> head(mutations)
                                                                              sampleID chr     pos ref mut
4 LP2000107-DNA_A01_vs_LP2000102-DNA_A01__pv.1.6__rg.grch37_g1k__al.bwa_mem__.snp.pass   1  920552   G   A
5 LP2000107-DNA_A01_vs_LP2000102-DNA_A01__pv.1.6__rg.grch37_g1k__al.bwa_mem__.snp.pass   1 1350208   G   A
6 LP2000107-DNA_A01_vs_LP2000102-DNA_A01__pv.1.6__rg.grch37_g1k__al.bwa_mem__.snp.pass   1 1447367   T   G
7 LP2000107-DNA_A01_vs_LP2000102-DNA_A01__pv.1.6__rg.grch37_g1k__al.bwa_mem__.snp.pass   1 1909310   G   A
8 LP2000107-DNA_A01_vs_LP2000102-DNA_A01__pv.1.6__rg.grch37_g1k__al.bwa_mem__.snp.pass   1 2172675   G   C
9 LP2000107-DNA_A01_vs_LP2000102-DNA_A01__pv.1.6__rg.grch37_g1k__al.bwa_mem__.snp.pass   1 2846623   C   T
> 

> dim(mutations)
[1] 3574407       5
>

I want to change name of sample from 1 to 139 in R or Linux terminal but I don't know how to do that, any help please?

Thanks

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1 Answer 1

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I believe that 

uniqsampleID = 1:length(unique(mutations$sampleID))
names(uniqsampleID) = unique(mutations$sampleID)
mutations$sampleID = uniqsampleID[mutations$sampleID]

should work, assuming mutations is a data frame.

Explanation:

1:N creates a vector of length N, containing 1, 2, ..., N. So using 1:length(X) will do this for each item in X, so 1:length(unique(mutations$sampleID)) should give you a vector of 1:139.

Then names(uniqsampleID) = unique(mutations$sampleID) assigns to each of these numbers one of these sample IDs, which allows you to retrieve the sample number with uniqsampleID[mutations$sampleID].

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  • $\begingroup$ Sorry that gives 3574407 sample IDs while I only have 139 samples for each I have 25 chromosome and a lot of mutations; I mean sampleID must contains maximum 139 unique numbers $\endgroup$
    – Angel
    Nov 7, 2019 at 14:00
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    $\begingroup$ Ah I see! I'll change it. $\endgroup$
    – Whitehot
    Nov 7, 2019 at 14:02
  • $\begingroup$ Yessssss worked thanks; Sorry in chr column I have the number of chromosome 1:23 plus to X and Y; How I can add chr prefix to this column? I mean instead of 1 I should have chr1 $\endgroup$
    – Angel
    Nov 7, 2019 at 14:17
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    $\begingroup$ Technically should be another question, but paste0() can handle that. It would probably be mutations$chr = paste0("chr", mutations$chr) $\endgroup$
    – Whitehot
    Nov 7, 2019 at 14:24

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