[R] Deleting rows and store the deleted rows in new data frame

[Bansal, Vikas]

Thanks for your reply.
Can I use grep with numbers also?


 
5961     T 17  0  9
5962     T 17  0  9
5963     A 17  0  9
5964     G 13  0  10
5965     G 13  0  9
5966     G 13  0 13
5967     T 13  0  8
5968     T 13  0  5
5969     A 13  0 13
5970     G 13  0 13
5971     G 13  0  4
5972     G 13  0 13
5973     T 13  0 13

like in 5th column.If I want only rows whose value is more than 10 in 5th column?

Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
________________________________________
From: Phil Spector [spector at stat.berkeley.edu]
Sent: Monday, July 25, 2011 12:29 AM
To: Bansal, Vikas
Cc: r-help at r-project.org
Subject: Re: [R] Deleting rows and store the deleted rows in new data frame

There's no need to use sapply or loops with grep -- it's
already 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
                                         spector at stat.berkeley.edu


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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