mogsa {mogsa} | R Documentation |
The main function called by users, omics data analysis and gene set annotation.
A wrapper function of moa
and sup.moa
.
mogsa(x, sup, nf=NULL, factors = NULL, proc.row=NULL, w.data=NULL, w.row=NULL, statis=FALSE, ks.stat=FALSE, ks.B = 1000, ks.cores = NULL, p.adjust.method = "fdr")
x |
An object of class |
sup |
An object of class |
nf |
The number of principal components used to reconstruct, only used when x is a an object of |
factors |
The index of principal components used in the projection, used when non-consecutive PC to be included in the analysis. |
proc.row |
Preprocessing of rows. If x is a object of |
w.data |
Weights of datasets. If x is a object of |
w.row |
Weight of row. If x is a object of |
statis |
A logical indicates if statis algrithm should be used. If x is a object of |
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 |
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 |
p.adjust.method |
The method of p value adjustment, passed to |
A wrapper function of moa
and sup.moa
.
An object of class mgsa-class
.
This function will be changed to a generic function for "S4-style" programming.
Chen Meng
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.
# 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) mgsa1x <- mogsa(x = NCI60_4arrays, sup=NCI60_4array_supdata, factors = c(1,3,6), 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)