CODEWITHSUNDEEP
rregexbioinformaticssequencingvcf-variant-call-format
Kelly Williams
Kelly Williams

Reputation: 35

Using R for next-generation sequencing vcf files

I am an R beginner. I am using R to analyse my large next-generation sequencing vcf file and am having some difficulties. I have imported the very large vcf file as a data frame (2446824 obs. of 177 variables) and made a subset with just the 3 samples I am interested in (2446824 obs. of 29 variables).

I now wish to reduce the dimensions even further (reduce the rows to around 200000). I have been trying to use grep, but cannot get it to work. The error I get is 

Error in "0/1" | "1/0" : 
   operations are possible only for numeric, logical or complex types

Here is a small example part of the file I am working with.

Chr Start   End Ref Alt Func.refGene    INFO    FORMAT  Run.Sample1 Run.Sample2 Run.Sample3
489 1   909221  909221  T   C   PASS    GT:AD:DP:GQ:PL  0/1:11,0:11:33:0,33,381     ./.     ./.
490 1   909238  909238  G   C   PASS    GT:AD:DP:GQ:PL  0/1:11,6:17:99:171,0,274    0/1:6,5:11:99:159,0,116     1/1:0,15:15:36:441,36,0
491 1   909242  909242  A   G   PASS    GT:AD:DP:GQ:PL  0/1:16,4:13:45:0,45,532     0/0:11,0:11:30:0,30,366     0/0:16,0:17:39:0,39,479
492 1   909309  909309  T   C   PASS    GT:AD:DP:GQ:PL  0/0:23,0:23:54:0,54,700     0/0:15,1:16:36:0,36,463     0/0:19,0:19:48:0,48,598

There are two different ways in which I would like to reduce the rows in this dataset:

Code 1. If either $Run.Sample1 or $Run.Sample2 or $Run.Sample3 contains a “0/1” or “1/0” or “1/1” keep the entire row

Code 2. If $Run.Sample1 or $Run.Sample2 contain either a “0/1” or “1/0” or “1/1” and $Run.Sample3 contain “0/0” keep the entire row

The results I would want to get from code 1 are:

Chr Start   End Ref Alt Func.refGene    INFO    FORMAT  Run.Sample1 Run.Sample2 Run.Sample3
489 1   909221  909221  T   C   PASS    GT:AD:DP:GQ:PL  0/1:11,0:11:33:0,33,381     ./.     ./.
490 1   909238  909238  G   C   PASS    GT:AD:DP:GQ:PL  0/1:11,6:17:99:171,0,274    0/1:6,5:11:99:159,0,116     1/1:0,15:15:36:441,36,0
491 1   909242  909242  A   G   PASS    GT:AD:DP:GQ:PL  0/1:16,4:13:45:0,45,532     0/0:11,0:11:30:0,30,366     0/0:16,0:17:39:0,39,479

The results I would want to get from code 2 are:

Chr Start   End Ref Alt Func.refGene    INFO    FORMAT  Run.Sample1 Run.Sample2 Run.Sample3
489 1   909221  909221  T   C   PASS    GT:AD:DP:GQ:PL  0/1:11,0:11:33:0,33,381     ./.     ./.
491 1   909242  909242  A   G   PASS    GT:AD:DP:GQ:PL  0/1:16,4:13:45:0,45,532     0/0:11,0:11:30:0,30,366     0/0:16,0:17:39:0,39,479

Many thanks for your help

Kelly

Upvotes: 1

Views: 747

Answers (1)

akrun
akrun

Reputation: 887721

Try For the first case:

  dat[Reduce(`|`,lapply(dat[9:11], function(x) grepl("0/1|1/0|1/1", x))),]

For the second case based on the conditions mentioned:

 dat[ Reduce(`|`,lapply(dat[9:10], function(x) grepl("0/1|1/0|1/1", x))) 
              & grepl("0/0", dat[,11]),]

Update

 dat[ Reduce(`|`,lapply(dat[9:10], function(x) grepl("0/1|1/0|1/1", x))) 
       & grepl("\\.\\/\\.|0/0", dat[,11]),]

Upvotes: 5

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