Get distance to nearest TSS and gene id from AnnotationByGeneParts

Description

This accessor function gets the nearest TSS, its distance to target feature, strand and name of TSS/gene from AnnotationByGeneParts object

Usage

getAssociationWithTSS(x)

## S4 method for signature 'AnnotationByGeneParts'
getAssociationWithTSS(x)

Arguments

Value

RETURNS a data.frame containing row number of the target features, distance of target to nearest TSS, TSS/Gene name, TSS strand

Examples

data(cage)
bed.file = system.file("extdata/chr21.refseq.hg19.bed", package = "genomation")
gene.parts = readTranscriptFeatures(bed.file)
cage.annot = annotateWithGeneParts(cage, gene.parts, intersect.chr=TRUE)
head(getAssociationWithTSS(cage.annot))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(genomation)
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/genomation/AnnotationByGeneParts-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getAssociationWithTSS
> ### Title: Get distance to nearest TSS and gene id from
> ###   AnnotationByGeneParts
> ### Aliases: AnnotationByGeneParts-method getAssociationWithTSS
> ###   getAssociationWithTSS, getAssociationWithTSS,-methods
> ###   getAssociationWithTSS,AnnotationByGeneParts-method
> 
> ### ** Examples
> 
> data(cage)
> bed.file = system.file("extdata/chr21.refseq.hg19.bed", package = "genomation")
> gene.parts = readTranscriptFeatures(bed.file)
Reading the table... 
Calculating intron coordinates... 
Calculating exon coordinates... 
Calculating TSS coordinates... 
Calculating promoter coordinates... 
Outputting the final GRangesList... 

> cage.annot = annotateWithGeneParts(cage, gene.parts, intersect.chr=TRUE)
intersecting chromosomes...
> head(getAssociationWithTSS(cage.annot))
    target.row dist.to.feature feature.name feature.strand
323          1               0    NR_103796              +
7            2              49 NM_001204303              -
523          3             151    NM_004339              -
243          4              47 NM_001282907              -
233          5               0    NM_006988              -
292          6              16    NM_000454              +
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>