search for: sca_posit

Displaying 2 results from an estimated 2 matches for "sca_posit".

2011 Nov 21
1
coverage plot
Hi, I'm very beginner for R but I think it is a time to start as it is very useful. I have a coverage read file (illusmp454merCbed) for whole genome ~ 450 Mbp. This is head of this file. Scaffold sca_position coverage Scaffold1 1 0 Scaffold1 2 0 Scaffold1 3 0 Scaffold1 4 0 Scaffold1 5 0 Scaffold1 6 0 Scaffold1 7 1 Scaffold1 8 3 Scaffold1 9 3 I would like to plot everage coverage for every 1 kbp for whole genome. May I use R as below? Should I use IRanges? data <-read.table(file="~/q20snpref...
2011 Nov 26
1
plot xy data
...I have use this R script (as below), so I expect the plot is based on x axis, but the result was opposite. Any suggestion will be great. library(IRanges) data <-read.table(file="~/q20snpref/illusmp454merbed",sep="\t",header=F) colnames(data)<-c("Scaffold","sca_position","coverage") depth<-mean(data[,"coverage"]) #depth now has the mean (overall)coverage #set the bin-size window<-10001 rangefrom<-0 rangeto<-length(data[,"sca_position"]) data.10kb<-runmed(data[,"coverage"],k=window) png(file="cov_...