annmap.seqname: Seqnames manipulation functions

In annmap: Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

Description

These functions allow easier manipulation of the seqnames column of a GRanges object

Usage

  generalisedNameToNCBI( name, ... )
  generalisedNameToEnsembl( name, ... )
  seqnameMapping( x, mappingFunction, ... )
  seqnamesToNCBI( x )
  seqnamesToEnsembl( x )

Arguments

name	The name to convert.
x	A GRanges object to convert the seqnames of.
mappingFunction	The function to do the mapping of names.
...	Other arguments you may wish to send to a custom mapping function.

Details

These functions allow simple mapping between seqnames of a GRanges object.

The two standard derivations are seqnamesToNCBI and seqnamesToEnsembl. The rules for mapping are:

      Ensembl      NCBI
      1       <=>  chr1
      ...
      22      <=>  chr22
      X       <=>  chrX
      Y       <=>  chrY
      MT      <=>  chrM
  

You can define your own mapping function and pass it as the mappingFunction parameter to seqnameMapping function to do your own custom mapping.

The function seqnamesToNCBI calls seqnameMapping with generalisedNameToNCBI as the mappingFunction. The function seqnamesToEnsembl uses generalisedNameToEnsembl.

Author(s)

Tim Yates

Examples

  if(interactive()) {
    annmapConnect()
    seqnamesToNCBI( symbolToGene( c( 'tp53', 'shh' ) ) )
 }

annmap documentation built on Nov. 8, 2020, 7:43 p.m.