fastSeqPos2GenePos: Sequence Positon to GeneID and Details

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

Sequence Positon to GeneID and Details

Description

Map chromosomal sequences positions to their gene identifiers and positions

Usage

fastSeqPos2GenePos(seqid, seqbase)

Arguments

seqid	character vector of SeqID names
seqbase	integer vector of chromosomal sequence locations

Details

Given a set of SeqIDs and locations, like from an alignment program's output, map each of these to the appropriate GeneID, location within the gene, and that gene's location within its organism's GeneMap.

Value

A list with 4 elements:

GENE_ID	character vector of GeneIDs
GENE_POSITION	integer vector of gene-centric locations (relative to the forward strand, regardless of the gene's actual coding strand)
SPECIES	character vector of organism SpeciesIDs
GMAP_PTR	integer vector of row pointers into each appropriate GeneMap

Note

This routine only searches MapSets for organisms in the current target.

See Also

MapSets, for a detailed overview of organism annotation.

Examples

  fastSeqPos2GenePos( c("Pf3D7_02", "Hs_grc_11", "Pf3D7_12"), c( 118000, 12345678, 55000))

robertdouglasmorrison/DuffyTools documentation built on April 16, 2024, 6:31 a.m.