getVal(object,members): Retrieving values for given types from an object

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Description

Retrieving value of data-member from object

Usage

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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:

VN Format version
SO Sorting order

Valid values for sorting order (SO) are: unknown (default), unsorted, queryname or coordinate. Data members for class readGroup:

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

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).

Author(s)

Wolfgang Kaisers

Examples

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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)

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