tTFConstruct: Constrct a taxaTF object

In jingwyang/AnceTran: the R package for analyzing TF-binding evolution based on ChIP-seq data

Description

TFconstruct is a constructor function for taxaTF objects. This fuction takes in a binding score file and constructs a taxaTF object from which user can extract information for display or for further analysis.

Usage

tTFConstruct(BSFile = NULL, taxa = "all", tf = "all",
  verbose = FALSE)

Arguments

BSFile	a text file contains raw TF binding score values. Row names correspond with gene names, and colum names correspond with species and trasncription factor names.
taxa	one single string or a vector of strings specifying main taxa, such like species or celll line types, selected for constructing taxaTF object. If one single string "all" is given, all the taxa in the row names will be matched and selected ("all" by default).
tf	one single string or a vector of strings sepcifying transcription factor(s) selected for constructing taxaTF object. If one single string "all" is given, all the transcription factor(s) in the row names will be matched and selected ("all" by default).
verbose	a logical specifying whether to print more information on the screen while constructing taxaTF objects (FALSE by default).

Value

returns an object of class TaxaTF (S3 class, a list of taxonTF objects).

Examples

taxa.objects = tTFConstruct(BSFile =
   system.file('extdata/HNF4A_meanIntensity_4Mouse.txt', package = 'AnceTran'),
   taxa = "all", tf = "all", verbose = FALSE)

jingwyang/AnceTran documentation built on May 19, 2019, 2:57 a.m.