miniCofactorReport: Produces a miniCofactorReport

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

Description

This function allows you to get a PDF report of top cofactors along with DNA methylation information for a motif of a TF.

Usage

miniCofactorReport(
  TF,
  cell,
  filterBy = "mapped.peaks.ratio",
  threshold = 0,
  Methylation = TRUE,
  includeMotifOnly = TRUE,
  height = 12,
  width = 7,
  shufflesNumber = 100,
  shuffle_seed = 987,
  universe = NULL,
  tail = "lower",
  pAdjust = "BY",
  chromSizes = loadChromSizes("hg38"),
  byChrom = FALSE,
  included = 1,
  pdfName = NULL,
  server = "sg"
)

Arguments

TF	[character] Main TF of interest.
cell	[character] Cell of interest.
filterBy	[character] Threshold category to filter cobinding partners. Currently supported are: "mapped.peaks.ratio,effect.size,p.significance,p.value,q.significance,q.value,e.significance,e.value and fraction."
threshold	[numeric] Only the co-factors with co-binding percentages more than this threshold value will be reported. By default the threshold is 0.05.
Methylation	[logical] TRUE to retrieve cytosine methylation information.
includeMotifOnly	[logical] TRUE if you wish to include only peaks that contain the known binding motif.
height	[numeric] Height in inch for the plot.
width	[numeric] Width in inch for the plot.
shufflesNumber	The number of shuffled genomic regions to be created for theorical distribution (higher means more accurate).
shuffle_seed	The random seed to be used for shuffling.
universe	A set of genomic regions that prevent shuffles for occuring outside of it.
tail	If "lower" then, probabilities are P[X > x], if "higher", P[X <= x], if "both" then higher or lower is selected depending on the number of overlaps vs the theorical mean.
pAdjust	The method that will be used for correcting the p-values. BH, BY and bonferroni are available.
chromSizes	A vector containing all the chromosome lengths for the species in consideration.
byChrom	Will the shuffles stay in the chromosome they originate (TRUE) or can they be placed everywhere on the genome (FALSE)
included	Represents the fraction of each regions that can be outside of the universe.
pdfName	[character] Name of the pdf to be saved.
server	[character] server localtion to be linked, either 'sg' or 'ca'. for 'Singapore' or 'Canada', respectively.

Value

A PDF file with the cofactorReport.

Examples

miniCofactorReport(TF = "CEBPB",cell = "K562")

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