[R] Output for pasting multiple vectors
Spencer Brackett
@pbr@ckett20 @end|ng |rom @@|ntjo@ephh@@com
Tue Jun 25 21:32:42 CEST 2019
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.
>
[[alternative HTML version deleted]]
More information about the R-help
mailing list