rmTable: 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/rmTable.R

Description

Given an input of gene list, this function will do an integrative analysis including both MAP and MCMC. It will also give a summary table about the enriched gene sets.

Usage

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rmTable(idlist,
                      idtype=c("SYMBOL","ENTREZ","REFSEQ",
                     "ENSEMBL","ACCNUM","UNIPROT","PMID"),
                      symbol = TRUE,
                      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

symbol

logical; if TRUE, list gene symbols in set, otherwise list gene or probe ID

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. More imporantly, this function gives a summary data frame about the active gene sets, their GO terms, set size, number of associated genes included, and so on.

Value

The output is a list consisting of 4 parts: rm.table, rm.sol, bp.sol and incidence.mat.

rm.table

A data frame of active wholes (gene sets) ordered according to the posterior active probabilities.

rm.sol

the output of sequentialRM.

bp.sol

the output of bp.

incidence.mat

the incidence matrix and the response vector based on the input gene list

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"

## do not run
## res <- rmTable (idlist, lib="org.Hs.eg", n.upp=20, n.low=5, nupstart=10, by=1, alpha=0.00019, gamma=0.02279, p=0.00331)

wiscstatman/Rolemodel documentation built on May 4, 2019, 6:32 a.m.