Class "headerReadGroup": Representation of read - group data in header section of BAM files
headerReadGroup represents data contained in the header section of BAM-files.
Objects from the Class
Objects can be created by calls of the form
integer. Number of read groups.
integer. Number of different read group tags (currently = 12).
character. Read group identifier. Each read group must have an unique ID.
character. Name of sequencing center.
character. Date of run.
character. Flow order.
character. Array of nucleotide bases.
character. Programs used for processing.
character. Predicted median insert size.
character. Platform/technology for production of reads.
character. Unique platform identifier.
character. Sample name.
signature(object="headerReadGroup", l="list"): Adds new read group to object.
signature(x="headerReadGroup"): Returns data stored in this object as list.
signature(object="headerReadGroup"): Returns value of given segment.
signature(object="headerReadGroup"): Sets value of given segment.
signature(.Object="headerReadGroup"): Returns textual representation of data as specified in SAM Format.
The SAM Format Specification (v1.4-r985). The SAM Format Specification Working Group. September 7, 2011.
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bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools") reader<-bamReader(bam) isOpen(reader) header<-getHeader(reader) htxt<-getHeaderText(header) readGroup<-headerProgram(htxt) getVal(readGroup,"ID") setVal(readGroup,"ID","newID") l<-as.list(readGroup) txt<-getHeaderText(readGroup) bamClose(reader)
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