Hi Ryan, Michael, OK for unstrsplit. The generic is now in IRanges 1.21.18 (devel) with methods for ordinary list and CharacterList. There is also a method in Biostrings 2.31.6 (devel) for XStringSetList objects. See ?unstrsplit Cheers, H. On 12/16/2013 06:51 PM, Michael Lawrence wrote: > Btw, the name strunsplit is way better than my pasteCollapse. Maybe > tweak it to unstrsplit? Feels more like a verb. > > > > On Mon, Dec 16, 2013 at 4:16 PM, Hervé Pagès <hpages at="" fhcrc.org=""> <mailto:hpages at="" fhcrc.org="">> wrote: > > Hi Ryan, > > Here is one way to do this using Biostrings: > > library(Biostrings) > > strunsplit <- function(x, sep=",") > { > if (!is(x, "XStringSetList")) > x <- Biostrings:::XStringSetList("__B", x) > if (!isSingleString(sep)) > stop("'sep' must be a single character string") > > ## unlist twice. > unlisted_x <- unlist(x, use.names=FALSE) > unlisted_ans0 <- unlist(unlisted_x, use.names=FALSE) > > ## insert 'seq'. > unlisted_x_width <- width(unlisted_x) > x_partitioning <- PartitioningByEnd(x) > at <- cumsum(unlisted_x_width)[-end(__x_partitioning)] + 1L > unlisted_ans <- replaceAt(unlisted_ans0, at, value=sep) > > ## relist. > ans_width <- sum(relist(unlisted_x_width, x_partitioning)) > x_eltlens <- width(x_partitioning) > idx <- which(x_eltlens >= 2L) > ans_width[idx] <- ans_width[idx] + (x_eltlens[idx] - 1L) * > nchar(sep) > relist(unlisted_ans, PartitioningByWidth(ans_width)__) > } > > Then: > > > x <- CharacterList(A=c("id35", "id2", "id18"), B=NULL, C="id4", > D=c("id2", "id4")) > > strunsplit(x) > A BStringSet instance of length 4 > width seq names > [1] 13 id35,id2,id18 A > [2] 0 B > [3] 3 id4 C > [4] 7 id2,id4 D > > I'll add this to Biostrings. > > Cheers, > H. > > > > On 12/16/2013 03:04 PM, Ryan C. Thompson wrote: > > Hi all, > > I have some annotation data in a DataFrame, and of course since > annotations are not one-to-one, some of the columns are > CharacterList or > similar classes. I would like to know if there is an efficient > way to > collapse a CharacterList to a character vector of the same > length, such > that for elements of length > 1, those elements are collapsed with a > given separator. The following is what I came up with, but it is > very > slow for large CharacterLists: > > library(stringr) > library(plyr) > flatten.CharacterList <- function(x, sep=",") { > if (is.list(x)) { > x[!is.na <http: is.na="">(x)] <- laply(x[!is.na > <http: is.na="">(x)], str_c, collapse=sep, > .parallel=TRUE) > x <- as(x, "character") > } > x > } > > -Ryan > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages at fhcrc.org <mailto:hpages at="" fhcrc.org=""> > Phone: (206) 667-5791 <tel:%28206%29%20667-5791> > Fax: (206) 667-1319 <tel:%28206%29%20667-1319> > > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319