runPINSPlus: Run PINSPlus method to get the subtyping results.

In GaoLabXDU/CEPICS: CEPICS: a comparison and evaluation platform for integration methods in cancer subtyping

Description

Using PINSPlus R package to get the subtyping results.

Usage

runPINSPlus(datalist, kMax = 5, agreementCutoff = 0.5, cores = 1)

Arguments

datalist	A list of different omics data. Each data in data list should be format as a data matrix with rows representing features and columns representing samples.
kMax	An integer value means the maximize number of clusters we will try.
agreementCutoff	agreement threshold to be considered consistent. Default value is 0.5. Please see PINSPlus package for more details.
cores	An integer value means the number of cores for parallel computing.

Value

The sample clustering results matrix.

References

Nguyen,T. et al. (2017) A novel approach for data integration and disease subtyping. Genome Res., 27, 2025-2039.

Examples

data(COAD_Methy, COAD_miRNA, COAD_mRNA)
datalist <- list(COAD_Methy, COAD_miRNA, COAD_mRNA)
res <- runPINSPlus(datalist, 5, 0.5)

GaoLabXDU/CEPICS documentation built on June 9, 2020, 2:31 a.m.