[R] Output for pasting multiple vectors
Spencer Brackett
@pbr@ckett20 @end|ng |rom @@|ntjo@ephh@@com
Tue Jun 25 21:41:13 CEST 2019
Doing so results in the following subset of my data...
>colnames(meth)[1:10]
[1] "sample.NA.NA.NANA" "TCGA.27.1832.01.NA.NA.NANA"
"TCGA.27.1831.01.NA.NA.NANA"
[4] "TCGA.28.5216.01.NA.NA.NANA" "TCGA.16.0846.01.NA.NA.NANA"
"TCGA.28.5218.01.NA.NA.NANA"
[7] "TCGA.06.0178.01.NA.NA.NANA" "TCGA.06.0238.01.NA.NA.NANA"
"TCGA.06.0125.01.NA.NA.NANA"
[10] "TCGA.06.0219.01.NA.NA.NANA"
On Tue, Jun 25, 2019 at 3:32 PM Spencer Brackett <
spbrackett20 using saintjosephhs.com> wrote:
> 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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