Output for pasting multiple vectors

Tue, Jun 25, 2019 11:50 AM

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

?s 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 at sapo.pt 
<mailto:ruipbarradas at 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

    ?s 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 at sapo.pt <mailto:ruipbarradas at sapo.pt>

     > <mailto:ruipbarradas at sapo.pt <mailto:ruipbarradas at 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
     >
     >? ? ??s 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 at saintjosephhs.com

    <mailto:spbrackett20 at saintjosephhs.com>

     >? ? ?<mailto:spbrackett20 at saintjosephhs.com

    <mailto:spbrackett20 at saintjosephhs.com>>

     >? ? ?<mailto:spbrackett20 at saintjosephhs.com

    <mailto:spbrackett20 at saintjosephhs.com>

     >? ? ?<mailto:spbrackett20 at saintjosephhs.com

    <mailto:spbrackett20 at 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 at sapo.pt <mailto:ruipbarradas at sapo.pt>

    <mailto:ruipbarradas at sapo.pt <mailto:ruipbarradas at sapo.pt>>

     >? ? ? >? ? ?<mailto:ruipbarradas at sapo.pt

    <mailto:ruipbarradas at sapo.pt> <mailto:ruipbarradas at sapo.pt
    <mailto:ruipbarradas at 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
     >? ? ? >
     >? ? ? >? ? ? ? ??s 16:11 de 25/06/19, Spencer Brackett escreveu:
     >? ? ? >? ? ? ? ? > c1 = strsplit(i,split ='.', fixed = T)[[1]]
     >? ? ? >
     >

Output for pasting multiple vectors

Thread (26 messages)