holistOmics: HolistOmics an application of NPC on omics datasets

In llrs/STATegRa: Classes and methods for multi-omics data integration

Description

This function is defunct. Use omicsNPC instead.

Usage

holistOmics(dataInput, dataTypes, comb.method = c("Fisher", "Liptak", "Tippett"),
               numPerm = 1000, numCores = 1, verbose = FALSE)

Arguments

dataInput	List of ExpressionSet objects, one for each data modality.
dataTypes	Character vector with possible values: 'RNA-seq', 'microarray'
comb.method	Character vector with possible values: 'Fisher', 'Liptak', 'Tippett', if more than one is specified, all will be used.
numPerm	Number of permutations
numCores	Number of CPU cores to use
verbose	Logical, if set to TRUE holistOmics prints out the step that it performs

Value

A data.frame

Author(s)

Nestoras Karathanasis

References

Pesarin, Fortunato, and Luigi Salmaso. Permutation tests for complex data: theory, applications and software. John Wiley & Sons, 2010.

Examples

# Load the data
data("TCGA_BRCA_Batch_93")
# Setting dataTypes, the first two ExpressionSets include RNAseq data,
# the third ExpressionSet includes Microarray data.
dataTypes <- c("RNAseq", "RNAseq", "Microarray")
# Setting methods to combine pvalues
comb.method = c("Fisher", "Liptak", "Tippett")
# Setting number of permutations
numPerm = 1000
# Setting number of cores
numCores = 1
# Setting holistOmics to print out the steps that it performs.
verbose = TRUE
# Run holistOmics analysis.
# The output is a data.frame of p-values.
# Each row corresponds to a gene name. Each column corresponds to a method
# used in the analysis.
## Not run: out <- holistOmics(dataInput = TCGA_BRCA_Data, dataTypes = dataTypes,
                            comb.method = comb.method, numPerm = numPerm,
                            numCores = numCores, verbose = verbose)
## End(Not run)

llrs/STATegRa documentation built on May 29, 2019, 3:42 a.m.