rbamtools (version 2.16.17)

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

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:

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).

Examples

# NOT RUN {
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)
# }