[R] splitting a dataframe in R based on multiple gene names in a specific column
Jim Lemon
drjimlemon at gmail.com
Sat Aug 26 11:53:58 CEST 2017
Very tidy. Amazing what is hidden away in R packages.
Jim
On Sat, Aug 26, 2017 at 5:26 AM, Jeff Newmiller
<jdnewmil at dcn.davis.ca.us> wrote:
> If row numbers can be dispensed with, then tidyr makes this easy with the
> unnest function:
>
> #####
> library(dplyr)
> #>
> #> Attaching package: 'dplyr'
> #> The following objects are masked from 'package:stats':
> #>
> #> filter, lag
> #> The following objects are masked from 'package:base':
> #>
> #> intersect, setdiff, setequal, union
> library(purrr)
> library(tidyr)
>
> df.sample.gene<-read.table(
> text="Chr Start End Ref Alt Func.refGene Gene.refGene
> 284 chr2 16080996 16080996 C T ncRNA_exonic GACAT3
> 448 chr2 113979920 113979920 C T ncRNA_exonic LINC01191,LOC100499194
> 465 chr2 131279347 131279347 C G ncRNA_exonic LOC440910
> 525 chr2 223777758 223777758 T A exonic AP1S3
> 626 chr3 99794575 99794575 G A exonic COL8A1
> 643 chr3 132601066 132601066 A G exonic ACKR4
> 655 chr3 132601999 132601999 A G exonic BCDF5,CDFG6",
> header=TRUE,stringsAsFactors=FALSE)
>
> df.sample.out <- ( df.sample.gene
> %>% mutate( Gene.refGene = strsplit( Gene.refGene
> , ","
> )
> )
> %>% unnest( Gene.refGene )
> )
> df.sample.out
> #> Chr Start End Ref Alt Func.refGene Gene.refGene
> #> 1 chr2 16080996 16080996 C T ncRNA_exonic GACAT3
> #> 2 chr2 113979920 113979920 C T ncRNA_exonic LINC01191
> #> 3 chr2 113979920 113979920 C T ncRNA_exonic LOC100499194
> #> 4 chr2 131279347 131279347 C G ncRNA_exonic LOC440910
> #> 5 chr2 223777758 223777758 T A exonic AP1S3
> #> 6 chr3 99794575 99794575 G A exonic COL8A1
> #> 7 chr3 132601066 132601066 A G exonic ACKR4
> #> 8 chr3 132601999 132601999 A G exonic BCDF5
> #> 9 chr3 132601999 132601999 A G exonic CDFG6
> #####
>
>
> On Wed, 23 Aug 2017, Jim Lemon wrote:
>
>> Hi Bogdan,
>> Messy, and very specific to your problem:
>>
>> df.sample.gene<-read.table(
>> text="Chr Start End Ref Alt Func.refGene Gene.refGene
>> 284 chr2 16080996 16080996 C T ncRNA_exonic GACAT3
>> 448 chr2 113979920 113979920 C T ncRNA_exonic LINC01191,LOC100499194
>> 465 chr2 131279347 131279347 C G ncRNA_exonic LOC440910
>> 525 chr2 223777758 223777758 T A exonic AP1S3
>> 626 chr3 99794575 99794575 G A exonic COL8A1
>> 643 chr3 132601066 132601066 A G exonic ACKR4
>> 655 chr3 132601999 132601999 A G exonic BCDF5,CDFG6",
>> header=TRUE,stringsAsFactors=FALSE)
>>
>> multgenes<-grep(",",df.sample.gene$Gene.refGene)
>> rep_genes<-strsplit(df.sample.gene$Gene.refGene[multgenes],",")
>> ngenes<-unlist(lapply(rep_genes,length))
>> dup_row<-function(x) {
>> newrows<-x
>> lastcol<-dim(x)[2]
>> rep_genes<-unlist(strsplit(x[,lastcol],","))
>> for(i in 2:length(rep_genes)) newrows<-rbind(newrows,x)
>> newrows$Gene.refGene<-rep_genes
>> return(newrows)
>> }
>> for(multgene in multgenes)
>> df.sample.gene<-rbind(df.sample.gene,dup_row(df.sample.gene[multgene,]))
>> df.sample.gene<-df.sample.gene[-multgenes,]
>> df.sample.gene
>>
>> I added a second line with multiple genes to make sure that it would
>> work with more than one line.
>>
>> Jim
>>
>>
>> On Wed, Aug 23, 2017 at 9:57 AM, Bogdan Tanasa <tanasa at gmail.com> wrote:
>>>
>>> I would appreciate please a suggestion on how to do the following :
>>>
>>> i'm working with a dataframe in R that contains in a specific column
>>> multiple gene names, eg :
>>>
>>>> df.sample.gene[15:20,2:8]
>>>
>>> Chr Start End Ref Alt Func.refGene
>>> Gene.refGene284 chr2 16080996 16080996 C T ncRNA_exonic
>>> GACAT3448 chr2 113979920 113979920 C T ncRNA_exonic
>>> LINC01191,LOC100499194465 chr2 131279347 131279347 C G
>>> ncRNA_exonic LOC440910525 chr2 223777758 223777758 T
>>> A exonic AP1S3626 chr3 99794575 99794575 G
>>> A exonic COL8A1643 chr3 132601066 132601066 A
>>> G exonic ACKR4
>>>
>>> How could I obtain a dataframe where each line that has multiple gene
>>> names
>>> (in the field Gene.refGene) is replicated with only one gene name ? i.e.
>>>
>>> for the second row :
>>>
>>> 448 chr2 113979920 113979920 C T ncRNA_exonic
>>> LINC01191,LOC100499194
>>>
>>> we shall get in the final output (that contains all the rows) :
>>>
>>> 448 chr2 113979920 113979920 C T ncRNA_exonic LINC01191
>>> 448 chr2 113979920 113979920 C T ncRNA_exonic LOC100499194
>>>
>>> thanks a lot !
>>>
>>> -- bogdan
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
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