initialize-PeakRefiner-method: initialize a new PeakRefiner

In jrboyd/peakrefine: Peak Refinement Metric Gathering and Evalutation by Motif Enrichment

Description

initialize a new PeakRefiner

Usage

## S4 method for signature 'PeakRefiner'
initialize(.Object, peak_set, bam_treat_file,
  bam_input_file, pwm, target_pwm_names, fragment_lengths = NULL,
  color_overrides = NULL, color_default = "black",
  auto_frag_len_FUN = NULL, output_prefix = NULL)

Arguments

.Object	empty PeakRefiner
peak_set	GRanges formatted peak set to calculate motifs on
bam_treat_file	.bam file of aligned reads from ChIP-seq pulldown. Index must be at .bam.bai
bam_input_file	.bam file of aligned reads from input control. Index must be at .bam.bai
pwm	Position Weight Matrix from PWMEnrich
target_pwm_names	names of PWMs to include in figures by default
fragment_lengths	fragment lengths to consider
color_overrides	character. colors to use for each item in fragment_lengths. should contain valid hex ("#000000") or R colors ("black") and be named with items in fragment_lengths. non-overriden items will be black.
color_default	single character. black.
auto_frag_len_FUN	function to use to auto calculate fragment length. must accept two argument, bam_file and peak_set.
output_prefix	prefix to use for output files.

Value

valid PeakRefiner

jrboyd/peakrefine documentation built on July 30, 2020, 7:13 p.m.