plotPeakProf2 {ChIPseeker}R Documentation

plotAvgProf2

Description

plot the profile of peaks automatically

Usage

plotPeakProf2(
  peak,
  upstream,
  downstream,
  conf,
  by,
  type,
  weightCol = NULL,
  TxDb = NULL,
  xlab = "Genomic Region (5'->3')",
  ylab = "Peak Count Frequency",
  facet = "none",
  free_y = TRUE,
  verbose = TRUE,
  nbin = NULL,
  ignore_strand = FALSE,
  ...
)

Arguments

peak

peak file or GRanges object

upstream

upstream position

downstream

downstream position

conf

confidence interval

by

one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR'

type

one of "start_site", "end_site", "body"

weightCol

column name of weight

TxDb

TxDb object

xlab

xlab

ylab

ylab

facet

one of 'none', 'row' and 'column'

free_y

if TRUE, y will be scaled by AvgProf

verbose

print message or not

nbin

the amount of nbines

ignore_strand

ignore the strand information or not

...

additional parameter

Value

ggplot object

Author(s)

G Yu, Ming Li


[Package ChIPseeker version 1.30.2 Index]