[R] grep won't work finding one column

[Kate Ignatius]

For example,

DF will usually have numerous columns with sample1.at sample1.dp
sample1.fg sample2.at sample2.dp sample2.fg and so on....

I'm running this code in R as part of a shell script which runs over
several different file sizes so sometimes it will come across a file
with one sample in it: i.e. sample1: when the R code runs through this
file... trying to grep out  the "sample1.at" column does not work and
it will halt and stop.

Here is some sample data... say I want to get out the AT_ only column....


Sample_1 AT_1
A/A RR
G/G AA
T/T AA
G/A RA
G/G RR
C/C AA
C/C AA
C/T RA
A/A AA
T/G RA

it will have a problem grepping out this single column.

On Tue, Oct 14, 2014 at 10:38 AM, John McKown
<john.archie.mckown at gmail.com> wrote:
> On Tue, Oct 14, 2014 at 9:23 AM, Kate Ignatius <kate.ignatius at gmail.com> wrote:
>> I'm having an issue with grep:
>>
>> I have numerous columns that end with .at... when I use grep like so:
>>
>> df[,grep(".at",colnames(df))]
>>
>> it works fine.  When I have one column that ends with .at, it does not
>> work.  Why is that?  As this is loop with varying number of columns
>> ending in .at I would like some code that would work with 1 to n
>> number of columns.
>>
>> Is there something more optimal than grep?
>>
>> Thanks!
>
> I can't answer your direct question. But do you realize that your code
> does not match your words? The grep show does not _only_ match columns
> who name end with the characters '.at'. It matches all column names
> which contain any character followed by the characters "at". To do the
> match with only columns whose names end with the characters ".at", you
> need: grep("\.at$",colnames(df)).
>
> You might want to post an example which fails. Just to be complete, be
> sure to use the dput() function so that it is easy for members of the
> group to cut'n'paste to get your data into our own R workspace.
>
> --
> There is nothing more pleasant than traveling and meeting new people!
> Genghis Khan
>
> Maranatha! <><
> John McKown