txFeatureOverlap: Calculate overlap with transcript features

In Bishop-Laboratory/RLSeq: RLSeq: An analysis package for R-loop mapping data

Calculate overlap with transcript features

Description

Tests the overlap of transcript features with supplied peaks. See details.

Usage

txFeatureOverlap(object, quiet = FALSE)

Arguments

object	An RLRanges object.
quiet	If TRUE, messages will be suppressed. Default: FALSE

Details

Method

Transcript annotations were curated as part of the RLBase-data workflow and are provided via RLHub::annotations.

In txFeatureOverlap, each annotation "type" (e.g., "Exons", "Introns", etc) is compared to the supplied RLRanges, yielding overlap statistics with the following procedure:

1. For each annotation type, the peaks are overlapped with the annotations.

2. Then the number of overlapping peaks is counted and summarised using a priority order. This order determines which feature is assigned to a peak when that peak overlaps multiple features. The order is "TSS", "TTS", "5'UTR", "3'UTR", "Exon", "Intron", "Intergenic".

Value

An RLRanges object containing the results of the enrichment test accessed via rlresult(object, "txFeatureOverlap"). The results are in tbl format.

Examples

# Example RLRanges dataset
rlr <- readRDS(system.file("extdata", "rlrsmall.rds", package = "RLSeq"))

# RL Region Test
txFeatureOverlap(rlr)

Bishop-Laboratory/RLSeq documentation built on Jan. 28, 2023, 11:38 p.m.