runAnalysis: Whole analysis of Regulatory Impact Factors (RIF) and Partial...

In cbiagii/ceTF: Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Whole analysis of Regulatory Impact Factors (RIF) and Partial Correlation and Information Theory analysis (PCIT)

Description

This function uses RIF and PCIT algorithms to run the whole pipeline analysis. The pipeline is composed by 4 steps:

1. Step 1: Data adjustment;

2. Step 2: Differential expression analysis;

3. Step 3: Regulatory Impact Factors analysis;

4. Step 4: Partial Correlation and Information Theory analysis.

Usage

runAnalysis(
  mat,
  conditions = NULL,
  lfc = 2.57,
  padj = 0.05,
  TFs = NULL,
  nSamples1 = NULL,
  nSamples2 = NULL,
  tolType = "mean",
  diffMethod = "Reverter",
  data.type = NULL
)

Arguments

mat	Count data where the rows are genes and coluns the samples (conditions).
conditions	A vector of characters identifying the names of conditions (i.e. c('normal', 'tumor')).
lfc	logFoldChange module threshold to define a gene as differentially expressed (default: 2.57).
padj	Significance value to define a gene as differentially expressed (default: 0.05).
TFs	A vector of character with all transcripts factors of specific organism.
nSamples1	Number of samples that correspond to first condition.
nSamples2	Number of samples that correspond to second condition.
tolType	Tolerance calculation type (see tolerance) (default: 'mean').
diffMethod	Method to calculate Differentially Expressed (DE) genes (see expDiff) (default: 'Reverter')
data.type	Type of input data. If is expression (FPKM, TPM, etc) or counts.

Value

Returns an CeTF class object with output variables of each step of analysis.

See Also

CeTF-class

Examples

data('simCounts')
out <- runAnalysis(mat = simCounts,
                   conditions=c('cond1', 'cond2'),
                   lfc = 3,
                   padj = 0.05,
                   TFs = paste0('TF_', 1:1000),
                   nSamples1 = 10,
                   nSamples2= 10,
                   tolType = 'mean',
                   diffMethod = 'Reverter',
                   data.type = 'counts')

cbiagii/ceTF documentation built on Feb. 6, 2023, 9:05 p.m.