[R] Output for pasting multiple vectors

[Spencer Brackett]

So I can run the suggested `stringsAsFactors=FALSE` argument following the
'colnames(meth)[1:10]' one I just used?

Best,

Spencer

On Tue, Jun 25, 2019 at 3:28 PM Jeff Newmiller <jdnewmil using dcn.davis.ca.us>
wrote:

> 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.
>

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