standardize_sites: Standardize genomic site positions within a dataset

In cnobles/gintools: Genomic DNA Integration Analysis Tools

Description

Given a GRanges object ...

Usage

standardize_sites(input.sites)

standardize_sites(input.sites, counts.col = "counts", min.gap = 1L, sata.gap = 5L)

Arguments

input.sites	GRanges object of sites to standardize.
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 combine sites.
sata.gap	integer maximum distance to consider combining sites.
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

standardize_sites returns a GRanges object where the site positions have been standardized with sites within the gap distance.

Author(s)

Christopher Nobles, Ph.D.

Examples

gr <- gintools:::generate_test_granges()

standardize_sites(gr)

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