grep won't work finding one column
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.
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Maranatha! <><
John McKown