annotate_to_gene_models: Annotate to gene models

Description Usage Arguments Value Examples

View source: R/genomic_region_annotation.R

Description

Annotate to gene models

Usage

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annotate_to_gene_models(gr, txdb, gene_model =c("tx", "gene"),
    species = "hg19", promoters_upstream = 2000, promoters_downstream = 200,
    annotation_type = c("percent", "number"),
    annotation_prefix = "overlap_to_")

Arguments

gr

a GRanges object

txdb

a TranscritpDb object. At least the object should contain 'gene_id', 'tx_name'. ('gene_id' and 'tx_name' columns are used to identify genes and transcripts)

gene_model

type of gene model. By transcripts or by genes

species

We need this information to find out proper intergenic regions

promoters_upstream

length of upstream promoter from TSS, pass to promoters

promoters_downstream

length of downstream promoter from TSS, pass o promoters

annotation_type

Pass to annotate_to_genomic_features

annotation_prefix

Pass to annotate_to_genomic_features

Value

Following columns are attached to gr:

nearest_tss

the nearest tss (depending on gene_model)

dist_to_tss

distance to the closest tss (depending on gene_model)

nearest_gm

the closest gene model (depending on gene_model)

dist_to_gm

distance to teh closest gene model (depending on gene_model)

prefix_to_exon

percent of the region which is covered by exon

prefix_to_intron

percent of the region which is covered by intron

prefix_to_promoter

percent of the region which is covered by promoter

prefix_to_intergenic

percent of the region which is covered by intergenic regions

prefix_to_fiveUTR

percent of the region which is covered by 5'UTR

prefix_to_threeUTR

percent of the region which is covered by 3'UTR

Examples

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# There is no example
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jokergoo/cotools documentation built on May 18, 2017, 6:05 a.m.