# [R] how to work with long vectors

Changbin Du changbind at gmail.com
Thu Nov 4 17:45:41 CET 2010

```Thanks, Jim!

This is not what I want,  What I want is calculate the percentage of reads
bigger or equal to that reads in each position.MY output is like the
following:
for row 1, all the reads is >= 4, so the cover_per is 100,
for row 2, 99 % reads >=4, so the cover_per is 99.
1       100     4
2        99     8
3        98    13
4        97    14
5        96    17
6        95    20

I attached the input file with this email. This file is only 100 rows, very
small. MY original data set is 3384766 rows.

>
sep="\t", skip=0, header=F,fill=T) #
> dim(matt)
[1] 3384766       2

Thanks so much for your time!

> dim(matt)
[1] 100   2
>
>
> #calculate the cumulative coverage.
> cover_per<-function (data) {
+ output<-numeric(0)
+ for (i in data) {
+           x<-(100*sum(ifelse(data >= i, 1, 0))/length(data))
+           output<-c(output, x)
+                 }
+ return(output)
+ }
>
>
> result<-cover_per(cover)
[1] 100  99  98  97  96  95
>
> final<-data.frame(result, cover)
>
1       100     4
2        99     8
3        98    13
4        97    14
5        96    17
6        95    20

On Thu, Nov 4, 2010 at 9:18 AM, jim holtman <jholtman at gmail.com> wrote:

> Is this what you want:
>
> > x
> 1   Contig79:1     4
> 2   Contig79:2     8
> 3   Contig79:3    13
> 4   Contig79:4    14
> 5   Contig79:5    17
> 6   Contig79:6    20
> 7   Contig79:7    25
> 8   Contig79:8    27
> 9   Contig79:9    32
> 10 Contig79:10    33
> 11 Contig79:11    34
> > x\$percent <- x\$reads / max(x\$reads) * 100
> > x
>            id reads   percent
> 1   Contig79:1     4  11.76471
> 2   Contig79:2     8  23.52941
> 3   Contig79:3    13  38.23529
> 4   Contig79:4    14  41.17647
> 5   Contig79:5    17  50.00000
> 6   Contig79:6    20  58.82353
> 7   Contig79:7    25  73.52941
> 8   Contig79:8    27  79.41176
> 9   Contig79:9    32  94.11765
> 10 Contig79:10    33  97.05882
> 11 Contig79:11    34 100.00000
>
>
> On Thu, Nov 4, 2010 at 11:46 AM, Changbin Du <changbind at gmail.com> wrote:
> > HI, Dear R community,
> >
> > I have one data set like this,  What I want to do is to calculate the
> > cumulative coverage. The following codes works for small data set (#rows
> =
> > 100), but when feed the whole data set,  it still running after 24 hours.
> > Can someone give some suggestions for long vector?
> >
> > id                reads
> > Contig79:1    4
> > Contig79:2    8
> > Contig79:3    13
> > Contig79:4    14
> > Contig79:5    17
> > Contig79:6    20
> > Contig79:7    25
> > Contig79:8    27
> > Contig79:9    32
> > Contig79:10    33
> > Contig79:11    34
> >
> >
> > sep="\t", skip=0, header=F,fill=T) #
> > dim(matt)
> > [1] 3384766       2
> >
> > matt_plot<-function(matt, outputfile) {
> >
> >
> >
> > #calculate the cumulative coverage.
> > + cover_per<-function (data) {
> > + output<-numeric(0)
> > + for (i in data) {
> > +           x<-(100*sum(ifelse(data >= i, 1, 0))/length(data))
> > +           output<-c(output, x)
> > +                 }
> > + return(output)
> > + }
> >
> >
> >  result<-cover_per(cover)
> >
> >
> > Thanks so much!
> >
> >
> > --
> > Sincerely,
> > Changbin
> > --
> >
> >        [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>
>
> --
> Jim Holtman
> Cincinnati, OH
> +1 513 646 9390
>
> What is the problem that you are trying to solve?
>

--
Sincerely,
Changbin
--

Changbin Du
DOE Joint Genome Institute
Bldg 400 Rm 457
2800 Mitchell Dr
Walnut Creet, CA 94598
Phone: 925-927-2856
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```