DEG_detection: DEG_detection

In mbeccuti/PGS: PGS-Peculiar Genes Selection: a feature selection procedure for binary classification tasks.

Description

DEG_detection uses 'limma' package to detect differentially expressed genes. It creates a matrix containing all the DEG detected in the gene expression data set in input using the contrast file.

Usage

DEG_detection(X,y)

Arguments

X	Gene expression matrix
y	contrast file

Value

DEG_detection returns DEGs_file, containing the gene expression of the DEG detected by 'limma' package.

The function also displays the number of DEGs detected.

Author(s)

Federica Martina

References

Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W and Smyth GK (2015). “limma powers differential expression analyses for RNA-sequencing and microarray studies.” Nucleic Acids Research, 43(7), pp. e47.

Examples

## The function is currently defined as
DEG_detection('Matrix_Genes', 'contrast_file')

mbeccuti/PGS documentation built on May 23, 2019, 9:34 a.m.