Mr. Barradas, Oh haha my mistake. The following is the output you requested....
[1] "sample.NA.NA.NANA" [2] "TCGA.27.1832.01.NA.NA.NANA" [3] "TCGA.27.1831.01.NA.NA.NANA" [4] "TCGA.28.5216.01.NA.NA.NANA" [5] "TCGA.16.0846.01.NA.NA.NANA" [6] "TCGA.28.5218.01.NA.NA.NANA" [7] "TCGA.06.0178.01.NA.NA.NANA" [8] "TCGA.06.0238.01.NA.NA.NANA" [9] "TCGA.06.0125.01.NA.NA.NANA" [10] "TCGA.06.0219.01.NA.NA.NANA" Best, Spencer On Tue, Jun 25, 2019 at 2:50 PM 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]] > > > > > > > > > > [[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.
