[R] Output for pasting multiple vectors

[Rui Barradas]

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 <ruipbarradas using sapo.pt 
> <mailto: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>
>      > <mailto: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>>
>      >     <mailto: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>>
>      >      >     <mailto: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]]
>      >      >
>      >
>