call_transcribed_intervals: Call continuous intervals of nascent transcription from...

In Maxim-Ivanov/TranscriptomeReconstructoR: Data-driven Annotation of the Transcriptome

Call continuous intervals of nascent transcription from NET-seq or GRO-seq data

Description

Call continuous intervals of nascent transcription from NET-seq or GRO-seq data

Usage

call_transcribed_intervals(
  cov,
  min_signal = 3,
  max_gapwidth = 250,
  min_width = 500
)

Arguments

cov	GRanges object.
min_signal	Positive integer.
max_gapwidth	Non-negative integer.
min_width	Positive integer.

Value

List of length 2:

1. GRanges object containing merged intervals of nascent transcription.

2. GRanges object containing low coverage sub-intervals (gaps) within the merged transcribed intervals.

Details

The input file is expected to be returned by the load_BAM_files(mode = "nascent") function. It contains sequencing coverage of the chromosomes by nascent RNA-seq reads. Continuous intervals of coverage (with values not less than min_signal) are merged if the distance between them does not exceed max_gapwidth bp. Finally, the merged intervals are filtered to have length not less than min_width.

Maxim-Ivanov/TranscriptomeReconstructoR documentation built on Oct. 3, 2023, 11:19 p.m.