t.org] On Behalf Of William Dunlap
> Sent: Friday, November 05, 2010 9:58 AM
> To: Changbin Du
> Cc: r-help@r-project.org
> Subject: Re: [R] how to work with long vectors
>
> The following cover_per_3 uses sorting to solve
> the problem more quickly. It still has room
>
0.02
> > identical(v_3,v)
> [1] TRUE
>
> Bill Dunlap
> Spotfire, TIBCO Software
> wdunlap tibco.com
>
> > -----Original Message-
> > From: r-help-boun...@r-project.org
> > [mailto:r-help-boun...@r-project.org] On Behalf Of Changbin Du
> > Sent: Frida
0.02
> identical(v_3,v)
[1] TRUE
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
> -Original Message-
> From: r-help-boun...@r-project.org
> [mailto:r-help-boun...@r-project.org] On Behalf Of Changbin Du
> Sent: Friday, November 05, 2010 9:14 AM
> To: Phil
Thanks Martin! I will try it and will let your guys know how it goes.
On Fri, Nov 5, 2010 at 9:42 AM, Martin Morgan wrote:
> On 11/05/2010 09:13 AM, Changbin Du wrote:
> > HI, Phil,
> >
> > I used the following codes and run it overnight for 15 hours, this
> morning,
> > I stopped it. It seems
On 11/05/2010 09:42 AM, Martin Morgan wrote:
> ## first time only
> source("http://bioconductor.org";)
oops, source("http://bioconductor.org/biocLite.R";)
> biocLite("IRanges")
>
> ##
> library(IRanges)
> contigs = IRanges(start=1, width=matt$reads)
> cvg = coverage(contigs) ## an RLE summarizi
On 11/05/2010 09:13 AM, Changbin Du wrote:
> HI, Phil,
>
> I used the following codes and run it overnight for 15 hours, this morning,
> I stopped it. It seems it is still not efficient.
>
>
>>
> matt<-read.table("/house/groupdirs/genetic_analysis/mjblow/ILLUMINA_ONLY_MICROBIAL_GENOME_ASSEMBLY/4
HI, Phil,
I used the following codes and run it overnight for 15 hours, this morning,
I stopped it. It seems it is still not efficient.
>
matt<-read.table("/house/groupdirs/genetic_analysis/mjblow/ILLUMINA_ONLY_MICROBIAL_GENOME_ASSEMBLY/4083340/STANDARD_LIBRARY/GWZW.994.5.1129.trim_69.fastq.1962
Thanks Phil, that is great! I WILL try this and let you know how it goes.
On Thu, Nov 4, 2010 at 10:16 AM, Phil Spector wrote:
> Changbin -
> Does
>
>100 * sapply(matt$reads,function(x)sum(matt$reads >=
> x))/length(matt$reads)
>
> give what you want?
>
>By the way, if you want to use
Changbin -
Does
100 * sapply(matt$reads,function(x)sum(matt$reads >= x))/length(matt$reads)
give what you want?
By the way, if you want to use a loop (there's nothing wrong with that),
then try to avoid the most common mistake that people make with loops in R:
having your result grow
Thanks Martin, I will try this.
On Thu, Nov 4, 2010 at 10:06 AM, Martin Morgan wrote:
> On 11/04/2010 09:45 AM, Changbin Du wrote:
> > Thanks, Jim!
> >
> > This is not what I want, What I want is calculate the percentage of
> reads
> > bigger or equal to that reads in each position.MY output is
On 11/04/2010 09:45 AM, Changbin Du wrote:
> Thanks, Jim!
>
> This is not what I want, What I want is calculate the percentage of reads
> bigger or equal to that reads in each position.MY output is like the
> following:
Hi Changbin -- I might be repeating myself, but the Bioconductor
packages IR
HI, Henrique,
Thanks for the great help!
I compared the output from your codes:
> te<-rev(100 * cumsum(matt$reads > 1) / length(matt$reads) )
> te
[1] 100 99 98 97 96 95 94 93 92 91 90 89 88 87 86 85 84
83
[19] 82 81 80 79 78 77 76 75 74 73 72 71 70 69 68 67 66
Thanks, Jim!
This is not what I want, What I want is calculate the percentage of reads
bigger or equal to that reads in each position.MY output is like the
following:
for row 1, all the reads is >= 4, so the cover_per is 100,
for row 2, 99 % reads >=4, so the cover_per is 99.
> head(final)
cove
Try this:
rev(100 * cumsum(matt$reads > 1) / length(matt$reads) )
On Thu, Nov 4, 2010 at 1:46 PM, Changbin Du wrote:
> HI, Dear R community,
>
> I have one data set like this, What I want to do is to calculate the
> cumulative coverage. The following codes works for small data set (#rows =
> 1
Is this what you want:
> x
id reads
1 Contig79:1 4
2 Contig79:2 8
3 Contig79:313
4 Contig79:414
5 Contig79:517
6 Contig79:620
7 Contig79:725
8 Contig79:827
9 Contig79:932
10 Contig79:1033
11 Contig79:1134
> x$percent <- x$re
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
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