[R] splitting a dataframe in R based on multiple gene names in a specific column

[Jim Lemon]

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]]
>
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