AssociateWithGenes: Associates a vector of probe positions with the nearest input...

In AffyTiling: Easy extraction of individual probes in Affymetrix tiling arrays

Description

Associates a vector of probes, with known genomic positions, to the nearest transcription start site (TSS).

If argument D is specified, returns ALL genes with a TSS < D bp from pID. Otherwise, the nearest gene is returned for each probe.

Returns vector composed of the following columns: ProbeID – Unique probe ID. GeneID – Gene/ transcript ID. pgDistance – Distance between ProbeID and GeneID TSS; Positive values indicate upstream of the TSS. Negative values indicate downstream.

Usage

AssociateWithGenes(kgID, kgCHR, kgSTR, kgSTART, kgEND, pID, pCHR, pMID, D=NULL)

Arguments

kgID	Vector of gene IDs, one for each transcription start site.
kgCHR	Vector of gene chromosomes, in the format "chr1", "chr2", ..., "chrX", "chrY".
kgSTR	Vector of strand: "+" for a gene on the "+1" strand, "-" for the "-1" strand.
kgSTART	Vector of start positions for each the transcript relative to the chromosome, NOT the start of transcription.
kgEND	Vector of end positions for each the transcript relative to the chromosome.
pID	Vector of UniqueIDs for each probe being evaluated.
pCHR	Vector of chromosomes, in the format "chr1", "chr2", ..., "chrX", "chrY".
pMID	Vector of start positions, one for each of the probes being annotated.
D	Threshold distance: if specified, returns all genes with a TSS < D bp from pID. Otherwise the nearest gene is returned for each probe.

Author(s)

Charles Danko

Examples

data(KnownGenes)

## Calculate the gene nearest to each probe in Einter data frame.
NearestGenes <- AssociateWithGenes(KG[,1], KG[,2], KG[,3], KG[,4], KG[,5], 
    Einter[,1], Einter[,3], (as.integer(Einter[,2])+13))

## Returns all genes within 1 Kb of each probe in Einter.
## Probes that do not have a gene within 1 Kb are not returned.
NearestGenes <- AssociateWithGenes(KG[,1], KG[,2], KG[,3], KG[,4], KG[,5], 
    Einter[,1], Einter[,3], (as.integer(Einter[,2])+13), D=1000)

AffyTiling documentation built on Oct. 5, 2016, 4:12 a.m.