Thanks Malcom. The documentation at this point is not accurate; there's a parameter count.mapped.reads=TRUE that needs to be set; it _is_ documented on ?BamFile and has been clarified in devel (where summarizeOverlaps is in the new package 'GenomicAlignments'). Martin ----- Malcolm Cook <mec at="" stowers.org=""> wrote: > Valerie and other Genomics, > > I read in ?summarizeOverlaps that > > 'colData' is a DataFrame with columns of 'object' (class of > 'reads') and 'records' (length of 'reads'). When 'reads' is a > BamFile or BamFileList the 'colData' holds the output of a call to > 'countBam' with columns of 'records' (total records in file), > 'nucleotides' and 'mapped'. The number in 'mapped' is the number > of records returned when 'isUnmappedQuery=FALSE' in the > 'ScanBamParam'. > > and also, > > ## When the reads are Bam files, the 'colData' contains summary > ## information from a call to countBam(). > > However, I find this NOT to be true. Viz (in a fresh R session) > > >library(GenomicRanges) > >example(summarizeOverlaps) > .... > > colData(se) > DataFrame with 2 rows and 0 columns > > # but yet: > > > do.call(rbind,lapply(fls,countBam)) > space start end width file records nucleotides > sm_treated1.bam NA NA NA NA sm_treated1.bam 1800 80260 > sm_untreated1.bam NA NA NA NA sm_untreated1.bam 1800 135000 > > Can you advise? > > Thanks! > > ~ Malcolm Cook > Computational Biology / Shilatifard Lab - Stowers Institute for Medical Research - Kansas City > > > PS > > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices datasets utils methods base > > other attached packages: > [1] edgeR_3.4.2 limma_3.18.9 DESeq_1.14.0 lattice_0.20-24 locfit_1.5-9.1 TxDb.Dmelanogaster.UCSC.dm3.ensGene_2.10.1 GenomicFeatures_1.14.2 AnnotationDbi_1.24.0 Biobase_2.22.0 pasillaBamSubset_0.0.8 BiocInstaller_1.12.0 Rsamtools_1.14.2 Biostrings_2.30.1 > [14] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.6 BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] annotate_1.40.0 biomaRt_2.18.0 bitops_1.0-6 BSgenome_1.30.0 DBI_0.2-7 genefilter_1.44.0 geneplotter_1.40.0 grid_3.0.2 RColorBrewer_1.0-5 RCurl_1.95-4.1 RSQLite_0.11.4 rtracklayer_1.22.2 splines_3.0.2 stats4_3.0.2 survival_2.37-7 tools_3.0.2 XML_3.98-1.1 xtable_1.7-1 zlibbioc_1.8.0 > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor