setVal: setVal(object,members,values): Setting values for given data...

In wokai/rbamtools: An R package for reading and writing BAM (Binary alignment) files.

Description

Setting values of data-members for object

Usage

setVal(object,members,values)

Arguments

object

An instance of class headerLine, headerReadGroup or headerProgram

members

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

values

Values that are written into data members

Details

The members and values (vectors) must have the same length.

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

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

wokai/rbamtools documentation built on May 4, 2019, 9:46 a.m.