rbamtools (version 2.4.0)

getVal: getVal(object,members)

Description

Retrieving value of data-member from object

Usage

getVal(object,member)

Arguments

object

An instance of class headerLine, headerReadGroup or headerProgram

member

A (character) member identifier corresponding to the data-members of the given object (e.g. PN for headerProgram)

Details

Data members for class headerLine: ll{ VN Format version SO Sorting order } Valid values for sorting order (SO) are: unknown (default), unsorted, queryname or coordinate.

Data members for class readGroup: ll{ ID Read Group identifier CN Name of sequencing center DS Description FO Flow order KS Nucleotides corresponding to key sequence of each read LB Library PG Programs used for processing the Read Group PI Predicted median insert size PL Sequencing Platform SM Sample name } Valid values for Sequencing Platform (PL) are: CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT or PACBIO.

Data members for class headerProgram ll{ ID Program record identifier PN Program name CL Command line PP Previous @PG-ID (Must match another ID in list) VN Program Version } Data members for refSeqDict can be accessed via data.frame generic functions (head,tail,[,[<-) or by conversion (as.data.frame).

Examples

library(rbamtools)
bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
reader<-bamReader(bam)
header<-getHeader(reader)
htxt<-getHeaderText(header)
hl<-headerLine(htxt)
getVal(hl,"SO")
bamClose(reader)