On Tue, 2009-04-28 at 16:58 +0000, [email protected] wrote: > Hello everybody, > > I am working with the yet unreleased package chipseq. > > There is a very nice xyplot that I am trying to reproduce from the > > http://www.bioconductor.org/workshops/2009/SeattleJan09/ChIP-seq/ChipSeqWorkflow.pdf > > However, R complains saying > > "Error in limits.and.aspect(prepanel.default.xyplot, prepanel = prepanel, : > need at least one panel" > > What am I doing? This > > > class(E1) > [1] "GenomeDataList" > attr(,"package") > [1] "BSgenome" > > names(E1) > [1] "C1" "C2" "T1" "T2" > > islandReadSummary <- function(x) > + { > + g <- extendReads(x, seqLen = 200) > + s <- slice(coverage(g, 1, max(end(g))), lower = 1) > + tab <- table(viewSums(s) / 200) > + ans <- data.frame(nread = as.numeric(names(tab)), count = as.numeric(tab)) > + ans > + } > > nread.islands <- as(gdApply(E1, islandReadSummary), "data.frame") > There were 50 or more warnings (use warnings() to see the first 50) > > xyplot(log(count) ~ nread | sample, > + nread.islands, > + subset = (chromosome == "chr19" & nread <= 40), > + layout = c(1, 4), pch = 16, type = c("p", "g")) > Error in limits.and.aspect(prepanel.default.xyplot, prepanel = prepanel, : > need at least one panel > > > > Can anybody shed some light?
What does return the command below ? str(subset(nread.islands, chromosome == "chr19" & nread <= 40)) > Clarification: the warning "There were 50 or more warnings (use warnings() to > see the first 50)" comes from IRanges. chipseq is using the slightly older > start/end convention rather than the newer shift/step convention. > > Thank you, > > Ivan > > > > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
