GSE.Test.Main: Gene-weighted pathway significance analysis
In GANPA: Gene Association Network-Based Pathway Analysis (GANPA)

Description Usage Arguments Value Author(s) References Examples

Test the significance of pathways in microarray experiments. This includes a network-based gene weighting algorithm for pathways. Classical and gene-weighted versions of gene set analysis approaches are both used. When required, this function also corrects for gene weighting biases caused by multiple-subunit protein.

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GSE.Test.Main(gExprs.obj, gsets, gNET, check.exprs = TRUE, msp.groups, 
			  size.min = 15, size.max = 500, permN = 1000, randN = 30, 
			  permFDR.cutoff = 0.5, output.label = "", msp.correction = TRUE)

`gExprs.obj`	Gene expression experiment data object.
`gsets`	A list of gene sets.
`gNET`	A gene association network stored in a list.
`check.exprs`	Logical (TRUE by default). Check and correct the missing values and scaling in the gExprs.obj. If the scale is natural, it will be converted to log2.
`msp.groups`	A list of multi-subunit proteins.
`size.min`	Minimum size of gene sets used for analysis. By default 15 genes.
`size.max`	Maximum size of gene sets used for analysis. By default 500 genes.
`permN`	Sample permutation times. By default 1000 times.
`randN`	Gene randomization times. Can be set smaller (say, 30) if you do not care randomization-based significance so as to be faster.
`permFDR.cutoff`	Sample permutation FDR cutoff. A number between 0 and 1. Set it larger if wish to see the significance of more gene sets.
`output.label`	A label to name output files, e.g. "P53\_C2".
`msp.correction`	Logical (TRUE). Whether to do a correction for multi-subunit proteins in gene weighting.

It will write analysis results to .csv files.

Zhaoyuan Fang, Weidong Tian and Hongbin Ji

Zhaoyuan Fang, Weidong Tian and Hongbin Ji. A Network-Based Gene Weighting Approach for Pathway Analysis. Submitted.

# Not to run
# library(GANPAdata)
# data("gExprs.p53", "gsets.msigdb.pnas", "gNET", "msp.groups", 
#      package="GANPAdata")
# GSE.Test.Main(gExprs.obj=gExprs.p53, gsets=gsets.msigdb.pnas, 
#      gNET=gNET, check.exprs=TRUE, msp.groups=msp.groups, 
#      size.min=15, size.max=500, permN=1000, randN=30, 
#      permFDR.cutoff=0.5, output.label="P53\_C2", msp.correction=TRUE)