R grep question

CRC$MMR.gene<-CRC$gene.all %in% match_strings
CRC$MMR.gene

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 at 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 at 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

?s 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