createFPWM: A function to generate an FPWM class object.

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

Description

This function assigns proper data to their associated slots of a S4 classe. This information is either provided by user, or exported from TFregulomeR's dataware using user specified data.

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 with the name of the main TF.
partners	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 with the name of the main TF.
forkPosition	This argument, defines from which point on, the matrix needs to be forked, or in the other words, up to which point two exclusive matrices need to be aggregated.
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

This component, returns a FPWM class object that can be used to plot or written in transfact format.

Examples

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

rtmag/FPWM documentation built on March 23, 2020, 12:46 a.m.