On 4/28/10 10:17 AM, James W. MacDonald wrote: > Hi Duke, > > Still the wrong list. You want Bioc-sig-sequencing. Thanks :D. I thought ShortRead (and other NGS packages) is in BioConductor group too, but I forgot cc'ing to bioc-sig-sequencing group. > > Duke wrote: >> Hi all, >> >> I am totally new to both R and BioConductor, so please be easy on me. >> I just updated my R package to 2.11, and installed new ShortRead >> package, but it seems that I am doing something wrong, and that there >> is some changes from ShortRead 1.5 to 1.6 (like the command format >> etc...). I tried to read a BAM file by creating a file as follow: > > You don't want the ShortRead package. You want Rsamtools, and the > scanBam() function. See ?scanBam for more info. Thanks for pointing this out. I will try Rsamtools. But readAligned does have *BAM* type now. How can I use it? D. > > Best, > > Jim > > >> >> library(ShortRead) >> sp <- SolexaPath('/Volumes/Data/analysis/glamblia/STATs') >> ap <- analysisPath(sp) >> (aln0 <- readAligned(ap, "WB4day.bwa.def.bam", "BAM")) >> >> but running the above just gave me the content of dirPath function. >> My package infos is: >> >> > sessionInfo() >> R version 2.11.0 (2010-04-22) >> x86_64-apple-darwin9.8.0 >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] ShortRead_1.6.0 Rsamtools_1.0.0 lattice_0.18-5 >> [4] Biostrings_2.16.0 GenomicRanges_1.0.1 IRanges_1.6.0 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.8.0 grid_2.11.0 hwriter_1.2 tools_2.11.0 >> >> Anybody has any idea? >> >> Thanks, >> >> D. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >