getTagMatrix: getTagMatrix

View source: R/tagMatrix.R

getTagMatrixR Documentation

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


GuangchuangYu/ChIPseeker documentation built on Oct. 31, 2024, 9:13 a.m.