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>>
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>> 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]]
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