mogsa: multiple omics data integration and gene set analysis

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/mogsa.R

Description

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

Usage

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  mogsa(x, sup, nf=NULL, proc.row=NULL, w.data=NULL, w.row=NULL, statis=FALSE, ks.stat=FALSE, ks.B = 1000, ks.cores = NULL)

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

ks.stat

The logical indicates if the p-value should be calculated using K-S statistic (the method used in "ssgsea" in GSVA package). Default is FALSE, which means using the z-score method. See sup.moa.

ks.B

An integer to indicate the number of bootstrapping samples to calculated the p-value of KS statistic.

ks.cores

An integer indicate the number of cores to be used in bootstrapping. It is passed to function mclapply in the parallel package.

Details

A wrapper function of moa and sup.moa.

Value

An object of class mgsa-class.

Note

This function will be changed to a generic function for "S4-style" programming.

Author(s)

Chen Meng

References

Preprint: Meng, C., Kuster, B., Peters, B., Culhane, AC., Moghaddas Gholami, A., moGSA: integrative single sample gene-set analysis of multiple omics data. doi: http://dx.doi.org/10.1101/046904 Haenzelmann, S., Castelo, R. and Guinney, J. GSVA: Gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics, 14:7, 2013. Barbie, D.A. et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature, 462(5):108-112, 2009.

See Also

moa and sup.moa

Examples

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  # 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)

mengchen18/mogsa documentation built on Nov. 23, 2017, 1:57 a.m.