[R] Output for pasting multiple vectors

[Jeff Newmiller]

A "very large" output from dput(head(meth)) may just mean that"meth" has factors instead of character columns. I recommend using the `stringsAsFactors=FALSE` argument if the data frame is being loaded using read.table or one of its variants. It almost always makes better sense to create factors explicitly after the data has been reviewed for validity.

On June 25, 2019 11:50:30 AM PDT, Rui Barradas <ruipbarradas using sapo.pt> wrote:
>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]]
>>      >      >
>>      >
>> 

-- 
Sent from my phone. Please excuse my brevity.