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>> 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>>>
> 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>>>
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]]
>
______________________________________________
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.
