annmap (version 1.14.0)

annmapSeqname: Seqnames manipulation functions

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.

Examples

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