Following code were taken from the 'rtracklayer' vignette, and will lead to an error message: #==================================================== library(rtracklayer) session <- browserSession() data(cpneTrack) track(session, "cpne2", autoScale = FALSE, yLineOnOff = TRUE, yLineMark = quantile(score(cpneTrack), 0.25)) <- cpneTrack ##Error in .local(object, con, variant, color, ...) : ##unused argument(s) (autoScale = FALSE, yLineOnOff = TRUE, yLineMark = view <- browserView(session, range(cpneTrack[1:5, ]), full = "cpne2") #Error in resolveTrackIndex(x, i) : Unknown tracks:cpne2 #In addition: Warning message: #closing unused connection 3 () #==================================================== and the following code does work, i.e. you must specify the 'format' as 'wig': track(session, "cpne2", format="wig",autoScale = FALSE, yLineOnOff = TRUE, yLineMark = quantile(score(cpneTrack), 0.25)) <- cpneTrack view <- browserView(session, range(cpneTrack[1:5, ]), full = "cpne2") #============================================================= sessionInfo() R version 2.10.0 Under development (unstable) (2009-09-14 r49685) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.5.15 RCurl_1.2-0 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] Biobase_2.5.7 Biostrings_2.13.43 BSgenome_1.13.14 IRanges_1.3.79 Rcompression_0.6-0 tools_2.10.0 [7] XML_2.6-0 --- LiGang

This was a bug in rtracklayer itself, not the vignette. It's fixed in 1.5.16. Thanks, Michael On Thu, Sep 24, 2009 at 8:53 PM, LiGang <luzifer.li@gmail.com> wrote: > > > Following code were taken from the 'rtracklayer' vignette, and will lead to > an > error message: > > #==================================================== > library(rtracklayer) > session <- browserSession() > data(cpneTrack) > > track(session, "cpne2", autoScale = FALSE, yLineOnOff = TRUE, > yLineMark = quantile(score(cpneTrack), 0.25)) <- cpneTrack > > ##Error in .local(object, con, variant, color, ...) : > ##unused argument(s) (autoScale = FALSE, yLineOnOff = TRUE, yLineMark = > > view <- browserView(session, range(cpneTrack[1:5, ]), full = "cpne2") > > #Error in resolveTrackIndex(x, i) : Unknown tracks:cpne2 > #In addition: Warning message: > #closing unused connection 3 () > #==================================================== > > > > and the following code does work, i.e. you must specify the 'format' as > 'wig': > > > track(session, "cpne2", format="wig",autoScale = FALSE, yLineOnOff = TRUE, > yLineMark = quantile(score(cpneTrack), 0.25)) <- cpneTrack > > view <- browserView(session, range(cpneTrack[1:5, ]), full = "cpne2") > > > > #============================================================= > sessionInfo() > R version 2.10.0 Under development (unstable) (2009-09-14 r49685) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.5.15 RCurl_1.2-0 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.5.7 Biostrings_2.13.43 BSgenome_1.13.14 > IRanges_1.3.79 Rcompression_0.6-0 tools_2.10.0 > [7] XML_2.6-0 > > > --- > LiGang > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]