readReads: Read sequencing reads from either a BAM or a BED file.

In chandlerzuo/mbasic: Matrix Based Analysis for State-space Inference and Clustering.

Description

Read sequencing reads from either a BAM or a BED file.

Usage

readReads(reads, extended, fragLen = 200, pairedEnd = FALSE,
  use.names = FALSE, format)

Arguments

reads	The sequencing file.
extended	A boolean value for whether each read will be extended to the fragment length.
fragLen	A numeric value for the fragment length.
pairedEnd	A boolean value for whether the sequencing file is paired end.
use.names	A boolean value to be passed to GenomicRanges functions.
format	A string of file format. Must be either 'BAM' or 'BED'.

Value

A RangedData object.

Author(s)

Samuel Younkin [e-mail]

chandlerzuo/mbasic documentation built on May 13, 2019, 3:24 p.m.