[R] Output for pasting multiple vectors

[Rui Barradas]

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 <ruipbarradas using sapo.pt 
> <mailto:ruipbarradas using 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
>      > <spbrackett20 using saintjosephhs.com
>     <mailto:spbrackett20 using saintjosephhs.com>
>     <mailto:spbrackett20 using saintjosephhs.com
>     <mailto:spbrackett20 using 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
>     <ruipbarradas using sapo.pt <mailto:ruipbarradas using sapo.pt>
>      >     <mailto:ruipbarradas using sapo.pt <mailto:ruipbarradas using 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]]
>      >
>