calc_v: Calculate distances of Tn5 insertions from motif.

In SamBuckberry/RunATAC: Functions for Importing, Processing, Analyzing, Plotting and Reformatting ATAC-seq Data

Description

Calculate distances of Tn5 insertions from motif.

Usage

calc_v(frags_gr, motif_pos_gr, flank = 250, max_frag = 300)

Arguments

frags_gr	A GRanges object with ATAC-seq fragments. See the read_atac_frags function.
motif_pos_gr	A GRanges object with the positions of the PWM in ATAC-seq peaks. See the motif_gr function.
flank	Numeric of length 1. Number of bases flanking motif to plot.
max_frag	Integer of length 1. The maximum fragment size to include in plot.

Value

A data.frame with 2 columns. frag_size column contains the ATAC-seq fragment size. The distance column contains the distance from the fragment centure to the centre of the closest motif in motif_pos_gr.

SamBuckberry/RunATAC documentation built on Aug. 2, 2021, 9:54 a.m.