[BioC] sum of columns

[chris Jhon]

Hi Alex,
Thank you i used this

pos = rep(NA, nrow(D))
>
> for (i in 1:nrow(D)) {
> if(sum(D[i,-c(1,2)]) <0)  pos[i] = i
> }

and it is working and i can get all !is.na and put them is vector P

P=pos[!is.na(pos)]

The subset can not work i got the error
Error: memory exhausted (limit reached?)

ANy idea??
Thank you very much
On 7/11/13, Alessandro Brozzi <alessandro.brozzi at gmail.com> wrote:
> you might try to allocate first an empty vector of NA and then use a for
> loop:
>
> pos = rep(NA, nrow(D))
>
> for (i in 1:nrow(D)) {
> if(sum(D[i,-c(1,2)]) <0)  pos[i] = i
> }
>
> the subset:
>
> D[ pos[!is.na(pos)] , ]
>
> should be what you are seeking.
>
> hth,
> alex
>
> On Thu, Jul 11, 2013 at 11:22 AM, chris Jhon <cjhon217 at gmail.com> wrote:
>
>> Thank you very much ,However, I got an error
>> Error: cannot allocate vector of size 290 Kb
>>
>> > sessionInfo()
>> R version 2.14.0 (2011-10-31)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.14.0
>>
>> On 7/11/13, Alessandro Brozzi <alessandro.brozzi at gmail.com> wrote:
>> > D[ rowSums( D[ , -c(1,2) ] ) > 0 , ]
>> >
>> > where 1 and 2 are the indices of the non-numerical columns
>> >
>> >
>> > On Thu, Jul 11, 2013 at 11:12 AM, chris Jhon <cjhon217 at gmail.com>
>> > wrote:
>> >
>> >> Hi Alex,
>> >>
>> >> Thank you.
>> >>
>> >> However , i got error due to memory limit
>> >>
>> >> Error: memory exhausted (limit reached?)
>> >>
>> >> In addition i have one col that have no numerical vlaue (e.g gene
>> >> name) row sums will work only for numerical value columns?
>> >>
>> >> On 7/11/13, Alessandro Brozzi <alessandro.brozzi at gmail.com> wrote:
>> >> > let call D your dataframe then:
>> >> >
>> >> > D[ rowSums(D) > 0 , ]
>> >> >
>> >> > alex
>> >> >
>> >> >
>> >> > On Thu, Jul 11, 2013 at 10:56 AM, chris Jhon <cjhon217 at gmail.com>
>> >> > wrote:
>> >> >
>> >> >> Hi All,
>> >> >>
>> >> >> I have a data frame like this
>> >> >>
>> >> >>
>> >> >> gene         symbol    sample1 sample2 sample3 sample4
>> >> >>
>> >> >> gene1             A          0          0                0
>> >> >> 0
>> >> >> gene2             B          0          10              2
>>  0
>> >> >> gene3             C          0         0                0
>> >> >> 0
>> >> >>
>> >> >> and i would like to subset the data frame to have only genes that
>> have
>> >> >> sum in all samples greater than zero.
>> >> >>
>> >> >> How to do this in R
>> >> >>
>> >> >> Thank you for any help
>> >> >>
>> >> >> _______________________________________________
>> >> >> Bioconductor mailing list
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>> >> >>
>> >> >
>> >>
>> >
>>
>