getTagMatrix2: getTagMatrix2

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

getTagMatrix2

Description

Nested function for getTagMatrix() to deal with multiple windows

Usage

getTagMatrix2(
  peak,
  upstream,
  downstream,
  windows_name,
  type,
  by,
  TxDb = NULL,
  weightCol = NULL,
  nbin = NULL,
  verbose = TRUE,
  ignore_strand = FALSE
)

Arguments

peak	peak peak file or GRanges object
upstream	the distance of upstream extension
downstream	the distance of downstream extension
windows_name	the names of windows
type	one of "start_site", "end_site", "body"
by	one of 'gene', 'transcript', 'exon', 'intron', '3UTR' , '5UTR', or specified by users
TxDb	TxDb or self-made granges object, served as txdb
weightCol	column name of weight, default is NULL
nbin	the amount of nbines
verbose	print message or not
ignore_strand	ignore the strand information or not

Details

This is an internal function.

Value

tagMatrix

YuLab-SMU/ChIPseeker documentation built on Feb. 11, 2024, 5:22 p.m.