fastSeqPos2GenePos: Sequence Positon to GeneID and Details

Description Usage Arguments Details Value Note See Also Examples

Description

Map chromosomal sequences positions to their gene identifiers and positions

Usage

1
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

1
  fastSeqPos2GenePos( c("Pf3D7_02", "Hs_grc_11", "Pf3D7_12"), c( 118000, 12345678, 55000))

robertdouglasmorrison/DuffyTools documentation built on Dec. 14, 2018, 3:05 p.m.