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.
