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

Description Usage Arguments Details Author(s) Examples

Description

Setting values of data-members for object

Usage

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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

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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)
setVal(hl,"SO","coordinate")
bamClose(reader)

rbamtools documentation built on May 30, 2017, 3:26 a.m.

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