getTagMatrix: getTagMatrix

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

getTagMatrix

Description

calculate the tag matrix

Usage

getTagMatrix(
  peak,
  upstream,
  downstream,
  windows,
  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	a collection of region
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

getTagMatrix() function can produce the matrix for visualization. peak stands for the peak file. window stands for a collection of regions that users want to look into. Users can use window to capture the peak of interest. There are two ways to input window.

The first way is that users can use getPromoters()/getBioRegion()/makeBioRegionFromGranges() to get window and put it into getTagMatrix().

The second way is that users can use getTagMatrix() to call getPromoters()/getBioRegion()/makeBioRegionFromGranges(). In this way users do not need to input window parameter but they need to input txdb.

txdb is a set of packages contained annotation of regions of different genomes. Users can get the regions of interest through specific functions. These specific functions are built in getPromoters()/getBioRegion(). Many regions can not be gain through txdb, like insulator and enhancer regions. Users can provide these regions in the form of granges object. These self-made granges object will be passed to TxDb parameter and they will be passed to makeBioRegionFromGranges() to produce the window. In a word, TxDb parameter is a reference information. Users can pass txdb object or self-made granges into it.

Details see getPromoters,getBioRegion and makeBioRegionFromGranges

upstream and downstream parameter have different usages:

(1) window parameter is provided,

if type == 'body', upstream and downstream can use to extend the flank of body region.

if type == 'start_site'/'end_site', upstream and downstream do not play a role in getTagMatrix() function.

(2) window parameter is missing,

if type == 'body', upstream and downstream can use to extend the flank of body region.

if type == 'start_site'/'end_site', upstream and downstream refer to the upstream and downstream of the start_site or the end_site.

weightCol refers to column in peak file. This column acts as a weight vaule. Details see https://github.com/YuLab-SMU/ChIPseeker/issues/15

nbin refers to the number of bins. getTagMatrix() provide a binning method to get the tag matrix.

Value

tagMatrix

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