Hi,
Has anyone know about how to get the correct plot?
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_10k.png",width=1000,height=1000)
plot(x=data.10kb[rangefrom:rangeto],y=data[rangefrom:rangeto,"sca_position"],pch=".",cex=1,xlab="depth",ylab="bp_position",type="p")
dev.off()
Best regards,
Sutada
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