getReadLength: determine the most common read length for input bam_file....

In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

determine the most common read length for input bam_file. uses 50 randomly selected regions from query_gr. If fewer than 20 reads are present, loads all of query_gr.

Description

determine the most common read length for input bam_file. uses 50 randomly selected regions from query_gr. If fewer than 20 reads are present, loads all of query_gr.

Usage

getReadLength(bam_file, query_gr)

Arguments

bam_file	indexed bam file
query_gr	GRanges to read from bam file

Value

numeric of most common read length.

Examples

data(CTCF_in_10a_overlaps_gr)
qgr = CTCF_in_10a_overlaps_gr[1:5]
bam_file = system.file("extdata/test.bam", package = "seqsetvis", mustWork = TRUE)
getReadLength(bam_file, qgr)

jrboyd/seqsetvis documentation built on Dec. 10, 2024, 11:23 a.m.