annotate_to_gene_models: Annotate to gene models

In eilslabs/epic: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Annotate to gene models

Usage

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 TxDb 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 exons or number of exons overlapped to the region

'prefix_to'_intron

percent of the region which is covered by introns or number of introns overlapped to the region

'prefix_to'_promoter

percent of the region which is covered by promoters or number of promoters overlapped to the region

'prefix_to'_intergenic

percent of the region which is covered by intergenic regions or number of intergenic regions overlapped to the region

'prefix_to'_fiveUTR

percent of the region which is covered by 5'UTRs or number of 5'UTRs overlapped to the region

'prefix_to'_threeUTR

percent of the region which is covered by 3'UTRs or number of 3'UTRs overlapped to the region

Author(s)

Zuguang Gu <[e-mail]>

Examples

# There is no example
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eilslabs/epic documentation built on May 16, 2019, 1:24 a.m.