Doing so results in the following subset of my data... >colnames(meth)[1:10] [1] "sample.NA.NA.NANA" "TCGA.27.1832.01.NA.NA.NANA" "TCGA.27.1831.01.NA.NA.NANA" [4] "TCGA.28.5216.01.NA.NA.NANA" "TCGA.16.0846.01.NA.NA.NANA" "TCGA.28.5218.01.NA.NA.NANA" [7] "TCGA.06.0178.01.NA.NA.NANA" "TCGA.06.0238.01.NA.NA.NANA" "TCGA.06.0125.01.NA.NA.NANA" [10] "TCGA.06.0219.01.NA.NA.NANA"
On Tue, Jun 25, 2019 at 3:32 PM Spencer Brackett < spbracket...@saintjosephhs.com> wrote: > So I can run the suggested `stringsAsFactors=FALSE` argument following > the 'colnames(meth)[1:10]' one I just used? > > Best, > > Spencer > > On Tue, Jun 25, 2019 at 3:28 PM Jeff Newmiller <jdnew...@dcn.davis.ca.us> > wrote: > >> A "very large" output from dput(head(meth)) may just mean that"meth" has >> factors instead of character columns. I recommend using the >> `stringsAsFactors=FALSE` argument if the data frame is being loaded using >> read.table or one of its variants. It almost always makes better sense to >> create factors explicitly after the data has been reviewed for validity. >> >> On June 25, 2019 11:50:30 AM PDT, Rui Barradas <ruipbarra...@sapo.pt> >> wrote: >> >Hello, >> > >> >No, you have not understood, post the colnames, not the row.names. >> > >> >Run >> > >> >colnames(meth)[1:10] >> > >> >and post the output of that code line. >> > >> >Hope this helps, >> > >> >Rui Barradas >> > >> >Às 19:31 de 25/06/19, Spencer Brackett escreveu: >> >> The requested reprex.... >> >> >> >> Rendering reprex... >> >> Error in parse(text = x, keep.source = TRUE) : >> >> <text>:26:2: unexpected ')' >> >> 25: >> >> 26: 2) >> >> ^ >> >> >> >> And the subset of the data.... >> >> >> >> row.names = c(NA, 6L), class = "data.frame") >> >> >> >> Best, >> >> >> >> Spencer >> >> >> >> >> >> On Tue, Jun 25, 2019 at 2:25 PM Rui Barradas <ruipbarra...@sapo.pt >> >> <mailto:ruipbarra...@sapo.pt>> wrote: >> >> >> >> Hello, >> >> >> >> No I wasn't expecting a very large file. >> >> Try to make a reproducible example. If the problem seems to be >> >with the >> >> sapply/strsplit post a subset of the data like just some of the >> >> colnames: >> >> >> >> colnames(meth)[1:10] >> >> >> >> >> >> This would allow us to run the code you are having trouble with. >> >> >> >> >> >> Hope this helps, >> >> >> >> Rui Barradas >> >> >> >> Às 17:36 de 25/06/19, Spencer Brackett escreveu: >> >> > The result of dput(head(meth)) is a very large data >> >table/listing of >> >> > data by category of what I presume to be the data from the two >> >> TCGA .txt >> >> > files I referenced previously. Is this the output you were >> >expecting? >> >> > >> >> > On Tue, Jun 25, 2019 at 12:19 PM Rui Barradas >> >> <ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt> >> >> > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>>> >> >wrote: >> >> > >> >> > Hello, >> >> > >> >> > 1) That error comes from not closing }) after the paste() >> >> instruction. >> >> > The complete statement would be >> >> > >> >> > >> >> > colnames(meth) = sapply(colnames(meth), function(i){ >> >> > c1 = strsplit(i, split ='\\', fixed = T)[[1]] >> >> > c1[4] = paste(strsplit(c1[4],split = "",fixed = >> >> > T)[[1]][1:2],collapse >> >> > = "") >> >> > paste(c1,collapse = ".") >> >> > }) >> >> > >> >> > >> >> > 2) Can you post the output of the following? >> >> > >> >> > dput(head(meth)) >> >> > >> >> > >> >> > Hope this helps, >> >> > >> >> > Rui Barradas >> >> > >> >> > Às 16:58 de 25/06/19, Spencer Brackett escreveu: >> >> > > The following is what I have implemented thus far... >> >> > > >> >> > > The file object for the two files listed in lines 1-2 >> >was >> >> set in my >> >> > > working directory, and are under the folder "Vakul's >> >GBM >> >> Code"... >> >> > hence >> >> > > the source of the odd 'prefix' for .txt files shown >> >> > > >> >> > > >library(data.table)>.anno = as.data.frame(fread(file >> >= >> >> > "~Vakul's GBM >> >> > > Code/mapper.txt", sep ="\t", header = T)) >> >> > > >meth = read.table(file = "~Vakul's GBM Code/GBM.txt", >> >> sep ="\t", >> >> > > header = T, row.names = 1) >> >> > > >meth = as.matrix(meth) >> >> > > >> >> > > ## the loop just formats the methylation column names >> >to >> >> match >> >> > format ## >> >> > > colnames(meth) = sapply(colnames(meth), function(i){ >> >> > > c1 = strsplit(i,split ='\\', fixed = T)[[1]] >> >> > > c1[4] = paste(strsplit(c1[4],split = "",fixed = >> >> > T)[[1]][1:2],collapse >> >> > > = "") >> >> > > paste(c1,collapse = ".") >> >> > > >> >> > > Rendering reprex... >> >> > > Error in parse(text = x, keep.source = TRUE) : >> >> > > <text>:28:0: unexpected end of input >> >> > > >> >> > > Best, >> >> > > >> >> > > Spencer >> >> > > >> >> > > >> >> > > >> >> > > On Tue, Jun 25, 2019 at 11:45 AM Spencer Brackett >> >> > > <spbracket...@saintjosephhs.com >> >> <mailto:spbracket...@saintjosephhs.com> >> >> > <mailto:spbracket...@saintjosephhs.com >> >> <mailto:spbracket...@saintjosephhs.com>> >> >> > <mailto:spbracket...@saintjosephhs.com >> >> <mailto:spbracket...@saintjosephhs.com> >> >> > <mailto:spbracket...@saintjosephhs.com >> >> <mailto:spbracket...@saintjosephhs.com>>>> >> >> > > wrote: >> >> > > >> >> > > Mr. Barradas, >> >> > > >> >> > > I got the same "output" as before, which is the + >> >> indicating that >> >> > > the expression is incomplete (according to some R >> >users >> >> > response in >> >> > > this chain). >> >> > > >> >> > > Should the argument perhaps be c1 = strsplit(i, >> >split >> >> = '\\', >> >> > fixed >> >> > > = T)[[1]] .... thereby eliminating the "." ? >> >> > > The reprex and error message as the result of this >> >is >> >> the same as >> >> > > the previous one I sent. >> >> > > >> >> > > I will send a more detailed description of what >> >code I >> >> have >> >> > done so >> >> > > far for context. >> >> > > >> >> > > Best, >> >> > > >> >> > > Spencer >> >> > > >> >> > > On Tue, Jun 25, 2019 at 11:30 AM Rui Barradas >> >> > <ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt> >> >> <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>> >> >> > > <mailto:ruipbarra...@sapo.pt >> >> <mailto:ruipbarra...@sapo.pt> <mailto:ruipbarra...@sapo.pt >> >> <mailto:ruipbarra...@sapo.pt>>>> >> >> > wrote: >> >> > > >> >> > > Hello, >> >> > > >> >> > > Maybe with >> >> > > >> >> > > c1 = strsplit(i, split = '\\.', fixed = T)[[1]] >> >> > > >> >> > > instead of split = '.' >> >> > > >> >> > > The dot is a metacharacter that matches any >> >> character so >> >> > it has >> >> > > to be >> >> > > escaped. >> >> > > >> >> > > Hope this helps, >> >> > > >> >> > > Rui Barradas >> >> > > >> >> > > Às 16:11 de 25/06/19, Spencer Brackett >> >escreveu: >> >> > > > c1 = strsplit(i,split ='.', fixed = T)[[1]] >> >> > > >> >> > >> >> >> >> -- >> Sent from my phone. Please excuse my brevity. >> > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
