plotAvgProf2: plotAvgProf

In YuLab-SMU/ChIPseeker: ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

plotAvgProf

Description

plot the profile of peaks that align to flank sequences of TSS

Usage

plotAvgProf2(
  peak,
  weightCol = NULL,
  TxDb = NULL,
  upstream = 1000,
  downstream = 1000,
  xlab = "Genomic Region (5'->3')",
  ylab = "Peak Count Frequency",
  conf,
  facet = "none",
  free_y = TRUE,
  verbose = TRUE,
  ignore_strand = FALSE,
  ...
)

Arguments

peak	peak file or GRanges object
weightCol	column name of weight
TxDb	TxDb object
upstream	upstream position
downstream	downstream position
xlab	xlab
ylab	ylab
conf	confidence interval
facet	one of 'none', 'row' and 'column'
free_y	if TRUE, y will be scaled by AvgProf
verbose	print message or not
ignore_strand	ignore the strand information or not
...	additional parameter

Details

This function is the old function of plotPeakProf2. It can only plot the start site region of gene.

Value

ggplot object

Author(s)

G Yu, Ming L

YuLab-SMU/ChIPseeker documentation built on Nov. 2, 2024, 1:45 p.m.