selectGene-methods: Gene selection using SPLS model
In sunny-zq/PICS: PICS (Pathway-guided Identification of Cancer Subgroups)

Description Usage Arguments Examples

Sparse Partial Least Square (SPLS) step for gene selection and dimension reduction.By applying SPLS to each pathway, we achieve the goal of gene selection and dimension reduction at the same time.

1
2
3

## S4 method for signature 'Prefiltered'
selectGene(object, fold = 5, K = 5,
  etas = seq(0.1, 0.9, 0.1), seed = 123)

`object`	output list of prefilter step
`fold`	The number of folds to use to perform the cross-validation process.
`K`	the maximum number of hidden features in spls.
`etas`	Thresholding parameter. eta should be between 0 and 1.
`seed`	random seed that was set, default = 123.

1
2
3

data(TCGA)
prefilter.results=prefilter( data=TCGA$geneexpr, time=TCGA$t, status=TCGA$d, plist=TCGA$pathList )
gene.results=selectGene( prefilter.results )