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? 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
