Rolemodel: One single call function to run both MAP and MCMC analysis...

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

View source: R/Rolemodel.R

Description

Given an input of gene list, this function will do an integrative analysis including both MAP and MCMC.

Usage

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Rolemodel(idlist, idtype=c("SYMBOL","ENTREZ","REFSEQ", "ENSEMBL","ACCNUM","UNIPROT","PMID"), 
lib, library.loc=NULL, n.upp=20, n.low=5, sets=c("GO","KEGG"), nupstart=10, by=1, alpha=0.01, gamma=0.02, p, nburn=1000000, 
ngen=10000000, sub=1000, penalty=5, initial="random", annotate=TRUE)

Arguments

idlist

character vector of gene ids for which to test enrichment of gene set categories

idtype

character, type of gene ids: SYMBOL, ENTREZID, REFSEQ, ENSEMBL, ACCNUM, UNIPROT, PMID. Default is SYMBOL

lib

character, organism library, e.g. "org.Hs.eg"

library.loc

character, location of library if local

n.upp

numeric, upper bound for number of genes in gene sets

n.low

numeric, lower bound for number of genes in gene sets

sets

character, GO or KEGG categories

...

for other arguments, see sequentialRM and bp

Details

This function actually integrates sequentialRM and bp. That is, given an input of gene list, which can be in gene symbos, Entrez ids, Ensembles, etc., this function will run both MAP and MCMC analysis. The output of MAP is ordered according to the active probability. With the help of this function, users could have total control of the parameters for the two functions sequentialRM and bp.

Value

The output is a list consisting of three parts: setprobs, rmsol and bpsol.

setprobs

A data frame of active wholes ordered according to the posterior active probabilities.

rmsol

the output of sequentialRM.

bpsol

the output of bp.

Author(s)

Zhishi Wang, Michael Newton and Subhrangshu Nandi.

References

Zhishi W., Qiuling H., Bret L. and Michael N.: A multi-functional analyzer uses parameter constaints to improve the efficiency of model-based gene-set analysis (2013).

See Also

sequentialRM, bp

Examples

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data(T2D_genelist)
idlist <- idlist[-57] ## no Entrez id for "KLHDC5"

## res <- Rolemodel (idlist, lib="org.Hs.eg", n.upp=20, n.low=5, nupstart=10, alpha=0.00019, gamma=0.02279, p=0.00331, ## nburn=1000000, ngen=10000000, sub=1000, penalty=5, initial="random", annotate=TRUE)

wiscstatman/Rolemodel documentation built on May 28, 2017, 4:34 a.m.