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

Description Usage Arguments Value Details

View source: R/Process_nascent_data.R

Description

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

Usage

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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 Jan. 28, 2021, 11:47 a.m.