[R] R grep question

[Jim Lemon]

Hi Kai,
You may find %in% easier than grep when multiple matches are needed:

match_strings<-c("MLH1","MSH2")
CRC<-data.frame(gene.all=c("MLH1","MSL1","MSH2","MCC3"))
CRC$MMR.gene<-ifelse(CRC$gene.all %in% match_strings,"Yes","No")

Composing your match strings before applying %in% may be more flexible
if you have more than one selection to make.

On Fri, May 28, 2021 at 1:57 AM Marc Schwartz via R-help
<r-help using r-project.org> wrote:
>
> Hi,
>
> A quick clarification:
>
> The regular expression is a single quoted character vector, not a
> character vector on either side of the | operator:
>
> "MLH1|MSH2"
>
> not:
>
> "MLH1"|"MSH2"
>
> The | is treated as a special character within the regular expression.
> See ?regex.
>
> grep(), when value = FALSE, returns the index of the match within the
> source vector, while when value = TRUE, returns the found character
> entries themselves.
>
> Thus, you need to be sure that your ifelse() incantation is matching the
> correct values.
>
> In the case of grepl(), it returns TRUE or FALSE, as Rui noted, thus:
>
>    CRC$MMR.gene <- ifelse(grepl("MLH1|MSH2",CRC$gene.all), "Yes", "No")
>
> should work.
>
> Regards,
>
> Marc Schwartz
>
>
> Kai Yang via R-help wrote on 5/27/21 11:23 AM:
> >   Hi Rui,thank you for your suggestion.
> > but when I try the solution, I got message below:
> >
> > Error in "MLH1" | "MSH2" :   operations are possible only for numeric, logical or complex types
> >
> > does it mean, grepl can not work on character field?
> > Thanks,Kai    On Thursday, May 27, 2021, 01:37:58 AM PDT, Rui Barradas <ruipbarradas using sapo.pt> wrote:
> >
> >   Hello,
> >
> > ifelse needs a logical condition, not the value. Try grepl.
> >
> >
> > CRC$MMR.gene <- ifelse(grepl("MLH1"|"MSH2",CRC$gene.all), "Yes", "No")
> >
> >
> > Hope this helps,
> >
> > Rui Barradas
> >
> > Às 05:29 de 27/05/21, Kai Yang via R-help escreveu:
> >> Hi List,
> >> I wrote the code to create a new variable:
> >> CRC$MMR.gene<-ifelse(grep("MLH1"|"MSH2",CRC$gene.all,value=T),"Yes","No")
> >>
> >>
> >> I need to create MMR.gene column in CRC data frame, ifgene.all column contenes MLH1 or MSH2, then the MMR.gene=Yes, if not,MMR.gene=No
> >>
> >> But, the code doesn't work for me. Can anyone tell how to fix the code?
> >>
> >> Thank you,
> >>
> >> Kai
>
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