annmap.coords: annmap co-ordinate mapping functions

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

Description

Functions to go between Genomic, Proteomic and Transcriptual co-ordinate systems.

Usage

  transcriptCoordsToGenome( transcript.ids, position=1, as.vector=FALSE, check.bounds=TRUE, truncate=TRUE, cds=FALSE )
  genomeToTranscriptCoords( position, transcript.ids, as.vector=FALSE, check.bounds=TRUE, end=c( 'none', 'both', '5', '3' ) )
  proteinCoordsToGenome( protein.ids, position=1, as.vector=FALSE, check.bounds=TRUE, truncate=TRUE )
  genomeToProteinCoords( position, protein.ids, as.vector=FALSE, check.bounds=TRUE )

Arguments

transcript.ids	A vector of transcript.ids (or a RangedData object of transcripts returned from another annmap function)
position	The position of interest (either a genomic position for both of the genomeToXXXX methods, or a protein or transcript sequence position for the other two methods )
as.vector	Should the returned data be in the form of a vector (if TRUE) or a RangedData object (if FALSE)
check.bounds	If TRUE, any postion outside the range of the protein/transcript will cause a warning to be issued and NA returned.
end	Should the UTR be taken in to account when calculating the location, one of ("none", "both", "3" or "5"). Defaults to none.
truncate	If truncate=TRUE, any lengths beyond the end of the transcript or protein will be set to the last residue
cds	If cds=TRUE then only the coding exons (or sub-regions of exons that are coding) are taken in to account.
protein.ids	A vector of protein.ids (or a RangedData object of proteins returned from another annmap function)

Details

The mapping functions need to deal with mappings that fall outside a transcript or protein (or within an intron). When as.vector=FALSE these are identified as NA in the results. Since RangedData objects cannot represent NA or missing values, when as.vector=FALSE, all locations which cannot be mapped are dropped from the result.

Author(s)

Tim Yates

See Also

annmapTo
annmapDetails
annmapAll
annmapRange
annmapFilters

Examples

  if(interactive()) {
    # Get the gene for 'tp53'
    gene        = symbolToGene( 'tp53' )
    # And the transcripts for this gene
    transcripts = geneToTranscript( symbolToGene( 'tp53' ) )
    # And the proteins for this transcript
    proteins    = transcriptToProtein( transcripts )

    # get the transcript coords for the transcripts of this gene, at the start of this gene
    genomeToTranscriptCoords( start( gene ), transcripts, as.vector=TRUE )
    #Returns a vector:
    # ENST00000413465 ENST00000359597 ENST00000504290 ENST00000510385 ENST00000504937
    #            1018              NA              NA              NA              NA     
    # ENST00000269305 ENST00000455263 ENST00000420246 ENST00000445888 ENST00000396473
    #              NA              NA              NA              NA              NA     
    # ENST00000545858 ENST00000419024 ENST00000509690 ENST00000514944 ENST00000505014
    #              NA              NA              NA              NA              NA
    # ENST00000414315 ENST00000508793 ENST00000503591 
    #              NA              NA              NA

    # With as.vector=FALSE
    genomeToTranscriptCoords( start( gene ), transcripts )
    # RangedData with 1 row and 1 value column across 1 space
    #             space       ranges | coord.space
    #       <character>    <IRanges> | <character>
    # 1 ENST00000413465 [1018, 1018] |  transcript

    genomeToProteinCoords( start( gene ), proteins, as.vector=TRUE )
    # ENSP00000410739 ENSP00000352610 ENSP00000269305 ENSP00000398846 ENSP00000391127
    #             340              NA              NA              NA              NA
    # ENSP00000391478 ENSP00000379735 ENSP00000437792 ENSP00000402130 ENSP00000425104
    #              NA              NA              NA              NA              NA
    # ENSP00000423862 ENSP00000394195 ENSP00000424104 ENSP00000426252 
    #              NA              NA              NA              NA 

    # With as.vector=FALSE
    genomeToProteinCoords( start( gene ), proteins )
    # RangedData with 1 row and 2 value columns across 1 space
    #             space     ranges |     frame coord.space
    #       <character>  <IRanges> | <numeric> <character>
    # 1 ENSP00000410739 [340, 340] |         0     protein
  }

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