get_genomic_context: Extraction of the genomic context

In InfOmics/LErNet: LErNet: characterization of lncRNAs via context-aware network expansion and enrichment analysis

Description

Retrieves the genomic context of input lncRNAs. The genomic context is defined as the set of protin coding genes that resides within a given range.

Usage

get_genomic_context(positions, lncgenes, pcgenes = NULL, max_window = 1e+05)

Arguments

positions	a data.frame reporting genomic positions by load_gtf. Columns are id type seqname start end. It may contain features into listed in lncgenes and pcgenes
lncgenes	a list of lncRNA genes
pcgenes	a list of protein-coding genes that are of interest for the study. If empty, the complete set of neighbors is extracted otherwise only pcgenes in this set are taken into account.
max_window	the maximum size of the genomic range

Value

a two column data.frame reporting neighborhood information. The first column gives lncRNAs and the second column gives their associated neighbors.

InfOmics/LErNet documentation built on April 10, 2021, 4:49 p.m.