# get the flags:
exons = getAnnotation("hg19","knownGene")
myflags = getFlags(regions = regions.merged.y, exons, "chrY", pctcut = 0.8)
... I am getting this fatal error ...
Error: length(unique(exons$chr)) == 1 is not TRUE
> length(unique(subset(x=exons, seqnames == "chrY", c(chr))))
[1] 1
> length(unique(unlist(subset(x=exons, seqnames == "chrY", c(chr)))))
[1] 101
> str(unique(unlist(subset(x=exons, seqnames == "chrY", c(chr)))))
chr [1:101] "100101116" "100101120" "100132596" "100133941" "100289150" ...
> summary(subset(x=exons, seqnames == "chrY", c(chr)))
chr
Length:1190
Class :character
Mode :character
> head(subset(x=exons, seqnames == "chrY"))
gene chr seqnames start end width strand
392 85 100101116 chrY 6258442 6258716 275 +
393 85 100101116 chrY 6262141 6262300 160 +
394 85 100101116 chrY 6269164 6269272 109 +
395 85 100101116 chrY 6271629 6271766 138 +
396 85 100101116 chrY 6279348 6279605 258 +
397 85 100101116 chrY 9590765 9591022 258 -
> tail(subset(x=exons, seqnames == "chrY"))
gene chr seqnames start end width strand
258853 22527 9189 chrY 2354455 2358810 4356 -
258854 22527 9189 chrY 2354455 2358813 4359 -
258855 22527 9189 chrY 2368352 2368580 229 -
258856 22527 9189 chrY 2368858 2369015 158 -
263606 22923 9426 chrY 20137667 20139627 1961 +
263607 22923 9426 chrY 19990140 19992100 1961 -
stopifnot(length(unique(exons$chr))==1,
length(unique(regions$chr)) == 1,
unique(exons$chr) == unique(regions$chr))
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C
[5] LC_MONETARY=C LC_MESSAGES=C LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] splines grid parallel stats4 stats graphics grDevices utils datasets
[10] methods base
other attached packages:
[1] rtracklayer_1.26.2 GenomicFeatures_1.18.3 AnnotationDbi_1.28.1
[4] derfinder_1.0.2 locfdr_1.1-7 devtools_1.7.0
[7] HiddenMarkov_1.8-1 Genominator_1.20.0 GenomeGraphs_1.26.0
[10] DESeq_1.18.0 lattice_0.20-29 locfit_1.5-9.1
[13] Biobase_2.26.0 edgeR_3.8.5 limma_3.22.4
[16] biomaRt_2.22.0 Rsamtools_1.18.2 Biostrings_2.34.1
[19] XVector_0.6.0 GenomicRanges_1.18.4 GenomeInfoDb_1.2.4
[22] IRanges_2.0.1 S4Vectors_0.4.0 BiocGenerics_0.12.1
[25] BiocInstaller_1.16.1 sqldf_0.4-10 gsubfn_0.6-6
[28] proto_0.3-10 RSQLite_1.0.0 DBI_0.3.1
loaded via a namespace (and not attached):
[1] BBmisc_1.9 BatchJobs_1.5 BiocParallel_1.0.3
[4] GenomicAlignments_1.2.1 RColorBrewer_1.1-2 RCurl_1.95-4.5
[7] XML_3.98-1.1 annotate_1.44.0 base64enc_0.1-2
[10] bitops_1.0-6 brew_1.0-6 checkmate_1.5.1
[13] chron_2.3-45 codetools_0.2-10 digest_0.6.8
[16] fail_1.2 foreach_1.4.2 genefilter_1.48.1
[19] geneplotter_1.44.0 httr_0.6.1 iterators_1.0.7
[22] sendmailR_1.2-1 stringr_0.6.2 survival_2.37-7
[25] tcltk_3.1.2 tools_3.1.2 xtable_1.7-4
[28] zlibbioc_1.12.0