Stage1_FeartureSelection {BioM2}

Stage 1 Fearture Selection

Description

Stage 1 Fearture Selection

Usage

Stage1_FeartureSelection(
  Stage1_FeartureSelection_Method = "cor",
  data = NULL,
  cutoff = NULL,
  featureAnno = NULL,
  pathlistDB_sub = NULL,
  MinfeatureNum_pathways = 10,
  cores = 1,
  verbose = TRUE
)

Arguments

Stage1_FeartureSelection_Method

Feature selection methods. Available options are c(NULL, 'cor', 'wilcox.test', 'cor_rank', 'wilcox.test_rank').

data

The input training dataset. The first column is the label.

cutoff

The cutoff used for feature selection threshold. It can be any value between 0 and 1. Commonly used cutoffs are c(0.5, 0.1, 0.05, 0.01, etc.).

featureAnno

The annotation data stored in a data.frame for probe mapping. It must have at least two columns named 'ID' and 'entrezID'. (For details, please refer to data( data("MethylAnno") )

pathlistDB_sub

A list of pathways with pathway IDs and their corresponding genes ('entrezID' is used). For details, please refer to ( data("GO2ALLEGS_BP") )

MinfeatureNum_pathways

The minimal defined pathway size after mapping your own data to pathlistDB(KEGG database/GO database).

cores

The number of cores used for computation.

verbose

Whether to print running process information to the console

Value

A list of matrices with pathway IDs as the associated list member names.

Author(s)

Shunjie Zhang

Examples

library(parallel)
data=MethylData_Test
feature_pathways=Stage1_FeartureSelection(Stage1_FeartureSelection_Method='cor',
                 data=data,cutoff=0,
                 featureAnno=MethylAnno,pathlistDB_sub=GO2ALLEGS_BP,cores=1)