Kurinji Pandiyan
2012-Jan-07 02:05 UTC
[R] Getting a list of unique gene names from a list with semi-colons
Hello, I have one column in my dataframe that has gene names of interest. Unfortunately, due to the fact that some probes lie between two genes or two transcripts of a gene, it looks something like this - FAM81A LOC283050;LOC283050;LOC283050;ZMIZ1 PINK1;PINK1 MRPL12;MRPL12 C1orf114 MMS19;UBTD1 I would like to know how to get a list with all the names with no semi-colons and removing the replicates. I would like the end result to look like - FAM81A LOC283050 ZMIZI PINK1 MRPL12 C1orf114 MMS19 UBTD1 Thanks a lot for your help! Kurinji [[alternative HTML version deleted]]
R. Michael Weylandt <michael.weylandt@gmail.com>
2012-Jan-07 02:17 UTC
[R] Getting a list of unique gene names from a list with semi-colons
I think you can do this with something like this (untested): unique(unlist(strsplit(XXX, ","))) Michael On Jan 6, 2012, at 8:05 PM, Kurinji Pandiyan <kurinji.pandiyan at gmail.com> wrote:> Hello, > > I have one column in my dataframe that has gene names of interest. > Unfortunately, due to the fact that some probes lie between two genes or > two transcripts of a gene, it looks something like this - > > FAM81A LOC283050;LOC283050;LOC283050;ZMIZ1 PINK1;PINK1 MRPL12;MRPL12 > C1orf114 MMS19;UBTD1 > I would like to know how to get a list with all the names with no > semi-colons and removing the replicates. I would like the end result to > look like - > > FAM81A > LOC283050 > ZMIZI > PINK1 > MRPL12 > C1orf114 > MMS19 > UBTD1 > > Thanks a lot for your help! > Kurinji > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org 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.
Gabor Grothendieck
2012-Jan-07 02:25 UTC
[R] Getting a list of unique gene names from a list with semi-colons
On Fri, Jan 6, 2012 at 9:05 PM, Kurinji Pandiyan <kurinji.pandiyan at gmail.com> wrote:> Hello, > > I have one column in my dataframe that has gene names of interest. > Unfortunately, due to the fact that some probes lie between two genes or > two transcripts of a gene, it looks something like this - > > ?FAM81A ?LOC283050;LOC283050;LOC283050;ZMIZ1 ?PINK1;PINK1 ?MRPL12;MRPL12 > C1orf114 ?MMS19;UBTD1 > I would like to know how to get a list with all the names with no > semi-colons and removing the replicates. I would like the end result to > look like - > > FAM81A > LOC283050 > ZMIZI > PINK1 > MRPL12 > C1orf114 > MMS19 > UBTD1 > > Thanks a lot for your help! > Kurinji >This uses strapply in gsubfn: x <- "FAM81A LOC283050;LOC283050;LOC283050;ZMIZ1 PINK1;PINK1" library(gsubfn) unique(strapply(x, "\\w+", c)[[1]]) If x is very long then there is a high speed version of strapply specialized to using c called strapplyc in the development version of gsubfn. For example, see this example of extracting 275,000 words from a novel: https://groups.google.com/group/corpling-with-r/msg/b85f7ff917cccb5d?dmode=source&output=gplain&noredirect&pli=1 -- Statistics & Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com
R. Michael Weylandt <michael.weylandt@gmail.com>
2012-Jan-07 02:29 UTC
[R] Getting a list of unique gene names from a list with semi-colons
Sorry. - that should be a semi-colon below. Michael Weylandt On Jan 6, 2012, at 8:17 PM, "R. Michael Weylandt <michael.weylandt at gmail.com>" <michael.weylandt at gmail.com> wrote:> I think you can do this with something like this (untested): > > unique(unlist(strsplit(XXX, ","))) > > Michael > > On Jan 6, 2012, at 8:05 PM, Kurinji Pandiyan <kurinji.pandiyan at gmail.com> wrote: > >> Hello, >> >> I have one column in my dataframe that has gene names of interest. >> Unfortunately, due to the fact that some probes lie between two genes or >> two transcripts of a gene, it looks something like this - >> >> FAM81A LOC283050;LOC283050;LOC283050;ZMIZ1 PINK1;PINK1 MRPL12;MRPL12 >> C1orf114 MMS19;UBTD1 >> I would like to know how to get a list with all the names with no >> semi-colons and removing the replicates. I would like the end result to >> look like - >> >> FAM81A >> LOC283050 >> ZMIZI >> PINK1 >> MRPL12 >> C1orf114 >> MMS19 >> UBTD1 >> >> Thanks a lot for your help! >> Kurinji >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help at r-project.org 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.