There's no need to use sapply or loops with grep -- it'salready vectorized. So you can find the rows you're interested in with
wh = grep('^[.,]+$',df[,9])
store them with
sf = df[wh,]
and delete them with
df = df[-wh,]
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
[email protected]
On Sun, 24 Jul 2011, Bansal, Vikas wrote:
Dear all,
I am using grep but I did not understand the problem as I am doing something
wrong.Please help me.
I am using this code-
sf=data.frame(sapply(df[],function(x) grep('\\.&\\,', df[,9])))
the thing is i have a data frame(df) like this-
10 135349467 g G 4 0 0 5 ,,,.,
10 135349468 t T 2 0 0 5 ,,c.,
10 135349469 g G 7 0 0 5 ,,a.,
10 135349470 c C 8 0 0 5 ,,,.,
10 135349471 a A 10 0 0 5 ,,,.,
10 135349472 g G 7 0 0 6 aa,.,,
10 135349473 g G 7 0 0 6 ,,c.,,
10 135349474 g G 4 0 0 6 ,,,.,,
10 135349475 a A 8 0 0 6 ,,,.,,
10 135349476 t T 1 0 0 6 g,,.,,
10 135349477 a A 7 0 0 6 ,,,.,,
10 135349478 a A 11 0 0 6 ,,,.,,
I want to delete those rows which contains only . and , in column 9.
and i want to store those rows in new data frame sf.
so my output should be-
df
10 135349468 t T 2 0 0 5 ,,c.,
10 135349469 g G 7 0 0 5 ,,a.,
10 135349472 g G 7 0 0 6 aa,.,,
10 135349473 g G 7 0 0 6 ,,c.,,
10 135349476 t T 1 0 0 6 g,,.,,
sf
10 135349467 g G 4 0 0 5 ,,,.,
10 135349470 c C 8 0 0 5 ,,,.,
10 135349471 a A 10 0 0 5 ,,,.,
10 135349474 g G 4 0 0 6 ,,,.,,
10 135349475 a A 8 0 0 6 ,,,.,,
10 135349477 a A 7 0 0 6 ,,,.,,
10 135349478 a A 11 0 0 6 ,,,.,,
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
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