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

setVal {rbamtools} | R Documentation

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

### 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)

[Package rbamtools version 2.16.17 Index]