getTagMatrix {ChIPseeker}R Documentation

getTagMatrix

Description

calculate the tag matrix

Usage

getTagMatrix(
  peak,
  upstream,
  downstream,
  windows,
  type,
  by,
  TxDb = NULL,
  weightCol = NULL,
  nbin = NULL,
  verbose = TRUE,
  flip_minor_strand = TRUE
)

Arguments

peak

peak peak file or GRanges object

upstream

the distance of upstream extension

downstream

the distance of downstream extension

windows

a collection of region

type

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

by

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

TxDb

TxDb

weightCol

column name of weight, default is NULL

nbin

the amount of nbines

verbose

print message or not

flip_minor_strand

whether flip the orientation of minor strand

Value

tagMatrix


[Package ChIPseeker version 1.30.0 Index]