Thank you! The following is the result of the corrected code using >cnames
....
> cnames
[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"
And then the first 2 lines of the output for the corrected paste() bit of
the original coding...
[[1]]
[1] "sample.NA.NA.NA"
[[2]]
[1] "TCGA.27.1832.01.NA.NA.NANA"
I would have to reconvene with my instructor who wrote the original code to
determine what his desired output for the data would be, but from what I
can tell, this bit of coding is formatting the given dataset(s) that we are
working with, prepping them for what will be a Linear regression model of
the protein expression datatype contained with the larger dataset. Sorry, I
know that this explanation doesn't really narrow things down.
For reference, here are the proceeding few lines of code following the
paste() function portion; specifically after the "})" ...
exp = read.table(file =
"/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/RNAseq/GBM.txt", sep = "\t",
header = T, row.names = 1)
exp = as.matrix(exp)
c = intersect(colnames(exp),colnames(meth))
exp = exp[,c]
meth = meth[,c]
m = apply(meth, 1, function(i){
log2(i/(1-i))
})
Best,
Spencer Brackett
On Tue, Jun 25, 2019 at 4:54 PM Rui Barradas <ruipbarra...@sapo.pt> wrote:
> Hello,
>
> The following works.
> First, get the colnames you have posted in a format that R can process.
> in your code you would skip this.
>
> cnames <- scan(what = character(), text = '
> "sample.NA.NA.NANA"
> "TCGA.27.1832.01.NA.NA.NANA"
> "TCGA.27.1831.01.NA.NA.NANA"
> "TCGA.28.5216.01.NA.NA.NANA"
> "TCGA.16.0846.01.NA.NA.NANA"
> "TCGA.28.5218.01.NA.NA.NANA"
> "TCGA.06.0178.01.NA.NA.NANA"
> "TCGA.06.0238.01.NA.NA.NANA"
> "TCGA.06.0125.01.NA.NA.NANA"
> "TCGA.06.0219.01.NA.NA.NANA"
> ')
> cnames
>
>
> Now your code corrected. I do not understand the output you are
> expecting. Can you give an example of the expected output of, say, the
> first 2 or 3 strings?
>
> lapply(cnames, function(i){
> c1 <- strsplit(i, split = '\\.')[[1]]
> c1[4] <- paste(strsplit(c1[4], split = "",fixed = T)[[1]][1:2],
> collapse = "")
> paste(c1, collapse = ".")
> })
>
>
> Hope this helps,
>
> Rui Barradas
>
> Às 20:24 de 25/06/19, Spencer Brackett escreveu:
> > Mr. Barradas,
> >
> > Oh haha my mistake. The following is the output you requested....
> >
> > [1] "sample.NA.NA.NANA"
> > [2] "TCGA.27.1832.01.NA.NA.NANA"
> > [3] "TCGA.27.1831.01.NA.NA.NANA"
> > [4] "TCGA.28.5216.01.NA.NA.NANA"
> > [5] "TCGA.16.0846.01.NA.NA.NANA"
> > [6] "TCGA.28.5218.01.NA.NA.NANA"
> > [7] "TCGA.06.0178.01.NA.NA.NANA"
> > [8] "TCGA.06.0238.01.NA.NA.NANA"
> > [9] "TCGA.06.0125.01.NA.NA.NANA"
> > [10] "TCGA.06.0219.01.NA.NA.NANA"
> >
> > Best,
> >
> > Spencer
> >
> > On Tue, Jun 25, 2019 at 2:50 PM Rui Barradas <ruipbarra...@sapo.pt
> > <mailto:ruipbarra...@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
> > <ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>
> > > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@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
> > > <ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>
> > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>>
> > > > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>
> > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@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
> > > > > <spbracket...@saintjosephhs.com
> > <mailto:spbracket...@saintjosephhs.com>
> > > <mailto:spbracket...@saintjosephhs.com
> > <mailto:spbracket...@saintjosephhs.com>>
> > > > <mailto:spbracket...@saintjosephhs.com
> > <mailto:spbracket...@saintjosephhs.com>
> > > <mailto:spbracket...@saintjosephhs.com
> > <mailto:spbracket...@saintjosephhs.com>>>
> > > > <mailto:spbracket...@saintjosephhs.com
> > <mailto:spbracket...@saintjosephhs.com>
> > > <mailto:spbracket...@saintjosephhs.com
> > <mailto:spbracket...@saintjosephhs.com>>
> > > > <mailto:spbracket...@saintjosephhs.com
> > <mailto:spbracket...@saintjosephhs.com>
> > > <mailto:spbracket...@saintjosephhs.com
> > <mailto:spbracket...@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
> > > > <ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>
> > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>>
> > > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>
> > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>>>
> > > > > <mailto:ruipbarra...@sapo.pt
> > <mailto:ruipbarra...@sapo.pt>
> > > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>>
> > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@sapo.pt>
> > > <mailto:ruipbarra...@sapo.pt <mailto:ruipbarra...@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]]
> > > > >
> > > >
> > >
> >
>
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