Try this: rev(100 * cumsum(matt$reads > 1) / length(matt$reads) )
On Thu, Nov 4, 2010 at 1:46 PM, Changbin Du <[email protected]> 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 > > > matt<-read.table("/house/groupdirs/genetic_analysis/mjblow/ILLUMINA_ONLY_MICROBIAL_GENOME_ASSEMBLY/4083340/STANDARD_LIBRARY/GWZW.994.5.1129.trim_69.fastq.19621832.sub.sorted.bam.clone.depth", > sep="\t", skip=0, header=F,fill=T) # > dim(matt) > [1] 3384766 2 > > matt_plot<-function(matt, outputfile) { > names(matt)<-c("id","reads") > > cover<-matt$reads > > > #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]] > > ______________________________________________ > [email protected] 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. > -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40" S 49° 16' 22" O [[alternative HTML version deleted]]
______________________________________________ [email protected] 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.
