David,
Right you are! Thanks for pointing that out.
strsplit <- 1:10
strsplit("With spaces", NULL)
strsplit
Jean
David Winsemius <[email protected]> wrote on 04/11/2012 01:17:07 PM:
> [image removed]
>
> Re: [R] strsplit help
>
> David Winsemius
>
> to:
>
> Jean V Adams
>
> 04/11/2012 01:19 PM
>
> Cc:
>
> alison waller, r-help
>
>
> On Apr 11, 2012, at 2:01 PM, Jean V Adams wrote:
>
> > Alison,
> >
> > Your code works fine on the first six lines of the data that you
> > provided.
> >
> > Rumino_Reps_agreeWalign <- data.frame(
> > geneid = c("657313.locus_tag:RTO_08940",
> > "457412.251848018",
> > "657314.locus_tag:CK5_20630",
> > "657323.locus_tag:CK1_33060",
> > "657313.locus_tag:RTO_09690",
> > "471875.197297106"),
> > count_Conser = c(7, 1, 2, 1, 3, 0),
> > count_NonCons = c(5, 4, 4, 0, 0, 2),
> > count_ConsSubst = c(5, 3, 1, 1, 3, 1),
> > count_NCSubst = c(1, 0, 0, 0, 1, 1))
> > gene.list <- strsplit(as.character(Rumino_Reps_agreeWalign$geneid),
> > "\\.")
> > Rumino_Reps_agreeWalignTR <- transform(Rumino_Reps_agreeWalign,
> > taxid=do.call(rbind, gene.list))
> >
> > Perhaps in later rows of the data there are cases where there is no
> > "." in
> > geneid? If not, can you provide a subset of your data that results
> > in the
> > warning? Use the dput() function.
> >
> > It's not a good idea to create an object named "strsplit". That
> > will only
> > mask the function strsplit() in later runs.
>
> There is not a problem with masking the function unless the new name
> is replaced with a language object (which wasn't the case here). The
> potential confusion is in minds of users. Function names are stored
> separately from non-language object names so you can have a data
> object named 'strsplit' and it will not mask the function 'strsplit'.
>
> --
> David.
> >
> > If time is an issue, a slightly faster way to do this, after the
> > strsplit() function is:
> > Rumino_Reps_agreeWalign$geneid.prefix <- sapply(gene.list, "[", 1)
> > Rumino_Reps_agreeWalign$geneid.suffix <- sapply(gene.list, "[", 2)
> >
> > Jean
> >
> >
> > alison waller wrote on 04/11/2012 08:23:29 AM:
> >
> >> Dear all,
> >>
> >> I want to use string split to parse column names, however, I am
> >> having
> >> some errors that I don't understand.
> >> I see a problem when I try to rbind the output from strsplit.
> >>
> >> please let me know if I'm missing something obvious,
> >>
> >> thanks,
> >> alison
> >>
> >> here are my commands:
> >>> strsplit<-strsplit(as.character(Rumino_Reps_agreeWalign$geneid),"\
> >>> \.")
> >>>
> >> Rumino_Reps_agreeWalignTR<-transform
> >> (Rumino_Reps_agreeWalign,taxid=do.call(rbind,
> >> strsplit))
> >> Warning message:
> >> In function (..., deparse.level = 1) :
> >> number of columns of result is not a multiple of vector length (arg
> > 1)
> >>
> >>
> >> here is my data:
> >>
> >>> head(Rumino_Reps_agreeWalign)
> >> geneid count_Conser count_NonCons
> >> count_ConsSubst
> >> 1 657313.locus_tag:RTO_08940 7
> >> 5 5
> >> 2 457412.251848018 1
> >> 4 3
> >> 3 657314.locus_tag:CK5_20630 2
> >> 4 1
> >> 4 657323.locus_tag:CK1_33060 1
> >> 0 1
> >> 5 657313.locus_tag:RTO_09690 3
> >> 0 3
> >> 6 471875.197297106 0
> >> 2 1
> >> count_NCSubst
> >> 1 1
> >> 2 0
> >> 3 0
> >> 4 0
> >> 5 1
> >> 6 1
> >>
> >> here are the results from strsplit:
> >>> head(strsplit)
> >> [[1]]
> >> [1] "657313" "locus_tag:RTO_08940"
> >>
> >> [[2]]
> >> [1] "457412" "251848018"
> >>
> >> [[3]]
> >> [1] "657314" "locus_tag:CK5_20630"
> >>
> >> [[4]]
> >> [1] "657323" "locus_tag:CK1_33060"
> >>
> >> [[5]]
> >> [1] "657313" "locus_tag:RTO_09690"
> >>
> >> [[6]]
> >> [1] "471875" "197297106"
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > [email protected] mailing list
> > 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.
>
> David Winsemius, MD
> West Hartford, CT
[[alternative HTML version deleted]]
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