[R] Output for pasting multiple vectors

[Spencer Brackett]

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 <ruipbarradas using 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 <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]]
> >      >
> >
>

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