mogsa (version 1.2.0)

mogsa: multiple omics data integration and gene set analysis

Description

The main function called by users, omics data analysis and gene set annotation. A wrapper function of moa and sup.moa.

Usage

mogsa(x, sup, nf=NULL, proc.row=NULL, w.data=NULL, w.row=NULL, statis=FALSE)

Arguments

x

An object of class list or moa-class. A list would be a list of data frame.

sup

An object of class list or moa.sup-class. A list would be a list of supplementary data.

nf

The number of principal components used to reconstruct, only used when x is a an object of list.

proc.row

Preprocessing of rows. If x is a object of list, it is passed moa

w.data

Weights of datasets. If x is a object of list, it is passed moa

w.row

Weight of row. If x is a object of list, it is passed moa

statis

A logical indicates if statis algrithm should be used. If x is a object of list, it is passed moa

Value

An object of class mgsa-class.

Details

A wrapper function of moa and sup.moa.

References

Not avaiable right now.

See Also

moa and sup.moa

Examples

  # library(mogsa)
  # loading gene expression data and supplementary data
  data(NCI60_4array_supdata)
  data(NCI60_4arrays)

  # using a list of data.frame as input
  mgsa1 <- mogsa(x = NCI60_4arrays, sup=NCI60_4array_supdata, nf=9,
                 proc.row = "center_ssq1", w.data = "inertia", statis = TRUE)
  # using moa as input
  ana <- moa(NCI60_4arrays, proc.row = "center_ssq1", w.data = "inertia", statis = TRUE)
  smoa <- sup.moa(ana, sup=NCI60_4array_supdata, nf=3)
  mgsa2 <- mogsa(x = ana, sup=NCI60_4array_supdata, nf=9)
  mgsa3 <- mogsa(x = ana, sup=smoa)