createFPWM: A function to generate an FPWM class object.

In rtmag/forkedTF: Creation of Forked-Position Weight Matrices, a graph model of multiple PWMs.

Description

This function creates the FPWM object and performs the fork in the motif.

Usage

createFPWM(
  mainTF = NULL,
  partners = NULL,
  cell = NULL,
  mainTF_MMID = NULL,
  partners_MMID = NULL,
  forkPosition = NULL,
  probabilityMatrix = FALSE,
  scaleFrequencyCounts = FALSE,
  flipMatrix = FALSE
)

Arguments

mainTF	[character] character with the name of the main TF.
partners	[character list or vector] List or character vector with the names of the partner TFs.
cell	[character] with the name of the main TF.
mainTF_MMID	[character] with the name of the main TF.
partners_MMID	[character vector] with the name of the main TF.
forkPosition	[numeric] defines the postion in the matrix where the motif will be forked.
probabilityMatrix	[logical] whether the function should return a frequency matrix or probability matrix (Default FALSE).
scaleFrequencyCounts	[logical] whether the count matrix should have equal rowSums across all the rows (Default FALSE).
flipMatrix	[logical] whether to apply reverse complement in case the core motif is after the forkPosition (Default FALSE).

Value

returns a FPWM class object that can be used to plot or write in transfact format.

Examples

fpwm <- createFPWM(mainTF ="CEBPB", partners = c("ATF4","ATF7","JUND","CEBPD"), cell = "K562", forkPosition = 5)

rtmag/forkedTF documentation built on Nov. 5, 2021, 10 a.m.