Hi Vikas,
The following works (I'm not very good with sapply, but the for loop
is ok if your data set is not huge).
> df <- read.table("test.txt",stringsAsFactors=FALSE)
> df
V1 V2 V3 V4 V5 V6 V7 V8 V9
1 10 135349467 g G 4 0 0 5 ,,,.,
2 10 135349468 t T 2 0 0 5 ,,c.,
3 10 135349469 g G 7 0 0 5 ,,a.,
4 10 135349470 c C 8 0 0 5 ,,,.,
5 10 135349471 a A 10 0 0 5 ,,,.,
6 10 135349472 g G 7 0 0 6 aa,.,,
7 10 135349473 g G 7 0 0 6 ,,c.,,
8 10 135349474 g G 4 0 0 6 ,,,.,,
9 10 135349475 a A 8 0 0 6 ,,,.,,
10 10 135349476 t T 1 0 0 6 g,,.,,
11 10 135349477 a A 7 0 0 6 ,,,.,,
12 10 135349478 a A 11 0 0 6 ,,,.,,
>
> df.rows <- c()
> counter <- 0
>
> for (i in 1:dim(df)[1]){
+ if(grepl('[[:alpha:]]',df[i,9])){
+ counter <- counter + 1
+ df.rows[counter] <- i
+ }
+ }
> sf <- df[-df.rows,]
> sf
V1 V2 V3 V4 V5 V6 V7 V8 V9
1 10 135349467 g G 4 0 0 5 ,,,.,
4 10 135349470 c C 8 0 0 5 ,,,.,
5 10 135349471 a A 10 0 0 5 ,,,.,
8 10 135349474 g G 4 0 0 6 ,,,.,,
9 10 135349475 a A 8 0 0 6 ,,,.,,
11 10 135349477 a A 7 0 0 6 ,,,.,,
12 10 135349478 a A 11 0 0 6 ,,,.,,
> df <- df[df.rows,]
> df
V1 V2 V3 V4 V5 V6 V7 V8 V9
2 10 135349468 t T 2 0 0 5 ,,c.,
3 10 135349469 g G 7 0 0 5 ,,a.,
6 10 135349472 g G 7 0 0 6 aa,.,,
7 10 135349473 g G 7 0 0 6 ,,c.,,
10 10 135349476 t T 1 0 0 6 g,,.,,
Steve
On Mon, Jul 25, 2011 at 7:32 AM, Bansal, Vikas <vikas.ban...@kcl.ac.uk> 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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