[R] Output for pasting multiple vectors

Spencer Brackett @pbr@ckett20 @end|ng |rom @@|ntjo@ephh@@com
Tue Jun 25 23:14:41 CEST 2019

```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 "})" ...

"/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 <ruipbarradas using 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,
>
>
> Às 20:24 de 25/06/19, Spencer Brackett escreveu:
> >
> > 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 <ruipbarradas using sapo.pt
> > <mailto: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,
> >
> >
> >     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
> 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,
> >      >
> >      >
> >      >     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
> >      >      >
> >      >      >     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?
> >      >      >
> >      >      >
> >      >      >
> >      >      >     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 =
> >      >      >     "~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>>>
> >      >      >     <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
> >     <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
> >      >      >      >     <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]]
> >      >      >      >
> >      >      >
> >      >
> >
>

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