On Thu, Jun 27, 2019 at 10:48 AM Spencer Brackett <
spbracket...@saintjosephhs.com> wrote:
> Hello,
>
> Was that helpful in clarifying?
>
> Best,
>
> Spencer
>
> On Tue, Jun 25, 2019 at 5:14 PM Spencer Brackett <
> spbracket...@saintjosephhs.com> wrote:
>
>> Thank you! The following is the result
Noted. Thank you as well! :)
On Tue, Jun 25, 2019 at 5:05 PM Richard O'Keefe wrote:
> This has nothing to do with your problem, but given the heavy use of "="
> to bind keyword parameters in R, I find the use of "=" for assignment as
> well confusing. It makes code harder to read than it needs
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.
This has nothing to do with your problem, but given the heavy use of "="
to bind keyword parameters in R, I find the use of "=" for assignment as
well confusing. It makes code harder to read than it needs to be.
The historic " <- " assignment makes the distinction obvious.
On Wed, 26 Jun 2019 at
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.
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" "TC
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
wrote:
> A "very large" output from dput(head(meth)) may just mean that"meth" has
> factors instead of character colum
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
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.N
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, ke
The requested reprex
Rendering reprex...
Error in parse(text = x, keep.source = TRUE) :
: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,
>
>
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
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 wrote:
> Hello,
>
> 1) That error com
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
= "")
p
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(fil
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 me
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
On 6/25/19 6:29 AM, Spencer Brackett wrote:
Mr. Barradas,
My apologies for the delayed response. No, (meth) is not a dataset within
CRAN. I’m not sure why my supervisor wrote that in as the object for the
bit of script I shared previously. Assuming that the correct object for
this particula
Hello,
The following is the bit of code I was having trouble with reproducing;
(meth) being the set matrix of the dataset I am working within R...
colnames(meth) = sapply(colnames(meth), function(i){
c1 = strsplit(i,split ='.', fixed = T)[[1]]
c1[4] = paste(strsplit(c1[4],split = "",fixed = T
Mr. Barradas,
My apologies for the delayed response. No, (meth) is not a dataset within
CRAN. I’m not sure why my supervisor wrote that in as the object for the
bit of script I shared previously. Assuming that the correct object for
this particular command is to be a data, the one with which we
Hello,
I cannot find the dataset. meth is a (CRAN) package dataset?
Rui barradas
Às 02:11 de 22/06/19, Spencer Brackett escreveu:
Hello,
I am attempting to paste multiple vectors using the paste() function for a
dataset that I'm working with. Shouldn't I be receiving some kind of
output as a
Note that just editing in R (or RStudio, or Notepad, or whatever) will not
solve the problem... you MUST learn how to use your email client to set the
format to send at least your R-help emails in plain text. If you don't do that,
the email program will just screw up your hard work.
I do think
Sent from my iPhone
> On Jun 21, 2019, at 6:48 PM, Spencer Brackett
> wrote:
>
> My apologies. Is there a way to edit this within R?
Most people use an editor or an IDE to work on their code. The code you
presented didn’t seem be doing what you were describing. You should put
together a
All the +-signs are telling you that the expression is not complete. Please
read the posting guide. I’m pretty sure you’ve already been warned NOT to use
html.
—
David.
Sent from my iPhone
> On Jun 21, 2019, at 6:11 PM, Spencer Brackett
> wrote:
>
> Hello,
>
> I am attempting to paste m
My apologies. Is there a way to edit this within R?
On Fri, Jun 21, 2019 at 9:47 PM David Winsemius
wrote:
> All the +-signs are telling you that the expression is not complete.
> Please read the posting guide. I’m pretty sure you’ve already been warned
> NOT to use html.
>
> —
> David.
>
> Sent
Would output <-paste() be part of the solution perhaps? Reading up on the
matter now.
Best,
Spencer
On Fri, Jun 21, 2019 at 9:11 PM Spencer Brackett <
spbracket...@saintjosephhs.com> wrote:
> Hello,
>
> I am attempting to paste multiple vectors using the paste() function for a
> dataset that I
Hello,
I am attempting to paste multiple vectors using the paste() function for a
dataset that I'm working with. Shouldn't I be receiving some kind of
output as a result of the following?
meth=as.matrix(meth)
> colnames(meth) = sapply(colnames(meth), function(i){
+ c1 = strsplit(i,split ='.', f
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