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 <tan...@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
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