Replacing some strings in R or terminal I have a .txt file; I have 139 unique sample IDs in sampleID column

&gt; 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
&gt; 

&gt; dim(mutations)
[1] 3574407       5
&gt; 


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
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].