summarizeOverlaps colData does NOT contain countBam() summary data
0
0
Entering edit mode
Malcolm Cook ★ 1.6k
@malcolm-cook-6293
Last seen 3 days ago
United States
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 >
• 655 views
ADD COMMENT

Login before adding your answer.

Traffic: 866 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6