RIF {CeTF} | R Documentation

## Regulatory Impact Factors (RIF) analysis

### Description

The RIF algorithm identify critical transcript factors (TF) from gene expression data.

### Usage

    RIF(input, nta = NULL, ntf = NULL, nSamples1 = NULL, nSamples2 = NULL)

### Arguments

`input` | A matrix of expression with differentially expressed genes and transcript factors in rows, and the samples in columns.
`nta` | Number of Differentially Expressed (DE) genes.
`ntf` | Number of Transcription Factors (TFs).
`nSamples1` | Number of samples of condition 1.
`nSamples2` | Number of samples of condition 2.

### Details

The input matrix must have the rows and columns ordered by the following request:

1. rows: DE genes followed by TFs;

2. columns: samples of condition1 followed by samples of condition2.

### Value

Returns an dataframe with the regulatory impact factors metric for each transcript factor.

### References

REVERTER, Antonio et al. Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data. Bioinformatics, v. 26, n. 7, p. 896-904, 2010. https://academic.oup.com/bioinformatics/article/26/7/896/212064

### Examples

    # load RIF input example
    data('RIF_input')

    # performing RIF analysis
    RIF_out <- RIF(input = RIF_input,
                   nta = 104,
                   ntf = 50,
                   nSamples1 = 10,
                   nSamples2 = 10)

[Package CeTF version 1.2.4 Index]