refine_breakpoints: Refine or resolve sonic break points within a dataset

In cnobles/gintools: Genomic DNA Integration Analysis Tools

Description

Given a GRanges object ....

Usage

refine_breakpoints(input.sites)

refine_breakpoints(input.sites, count = "counts", min.gap = 1L, sata.gap = 3L)

Arguments

input.sites	GRanges object. Ranges of alignments or sites to adjust.
counts.col	character string. Name of column holding range count information (ie. read counts). If not supplied, assume count of 1 for each row in sites.
min.gap	integer minimum gap to consider combining break points.
sata.gap	integer maximum distance to consider combining break points.
details	logical If TRUE, data columns will be appended to the metadata of the GRanges object noting the original and adjusted position for the site. FALSE by default.
quiet	logical during processing, should messages be suppressed which report findings? TRUE by default.

Details

refine_breakpoints returns a GRanges object where the sonic break point positions have been adjusted based on the dataset and counts.

Author(s)

Christopher L. Nobles, Ph.D.

Examples

gr <- gintools:::generate_test_granges()

refine_breakpoints(gr)

cnobles/gintools documentation built on Aug. 22, 2019, 10:36 a.m.