sequentialRM: The sequential approach

In atbroman/Rolemodel: Gene-set analysis via MFA-ILP

Description

Use the sequential approach introduced in the reference to speed up the running of integer linear programming (ILP).

Usage

sequentialRM(I, y, nupstart, by = 1, alpha, gamma, p)

Arguments

I	The incidence 0-1 matrix with unique row and column names, where rows are parts (genes) and columns are wholes (gene-sets).
y	Gene-level 0-1 data with the same names as the row names of I.
nupstart	The starting upper bound used in the sequential approach.
by	The increment of the upper bound used in the sequential approach, default value 1.
alpha	The false positive rate in role model, numeric value between 0 and 1. See reference.
gamma	The true positive rate in role model, numeric value between 0 and 1. See reference.
p	The prior active probability of wholes in role model, numeric value between 0 and 1. See reference.

Details

Generally, alpha and gamma can be estimated from the gene-level data by users themselves (see reference for examples), and alpha is less than gamma. p can be estimated via R package MGSA with alpha and gamma fixed.

We first perform the ILP on an initial incidence matrix (the smaller matrix) with lower bound equal lower bound of I and upper bound nupstart; then do another ILP, making use of the results obtained from the last ILP, on the bigger incidence matrix with upper bound equal nupstart + by. This process is repeated until the original incidence matrix I is reached. The suggested value for nupstart is 10. sequentialRM is our main function to perform the ILP calculation. ILP, shrinkRM and optimalRM are all invoked in this function.

Value

Return a list consisting of onwholes: the active wholes, i.e., the MFA-ILP (MAP) estimate, and sol: has the same structure with the output of ILP,

optimum	the value of the objective function at the optimum
solution	the vector of optimal coefficients (0-1vector)
status	an integer with status information about the solution returned. If the control parameter canonicalize_status is set (the default) then it will return 0 for the optimal solution being found, and non-zero otherwise. If the control parameter is set to FALSE it will return the GLPK status codes.

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).

Examples

data(t2d)

Isub <- subRM(t2d$I,5,20)
ysub <- t2d$y[rownames(Isub)]

## set the system parameters
alpha <- 0.00019
gamma <- 0.02279
p <- 0.00331

## use the sequential approach to get the MAP estimate on a smaller
## example of type 2 diabetes 
res <- sequentialRM(Isub, ysub, nupstart = 10, by =1, alpha, gamma, p)

atbroman/Rolemodel documentation built on May 10, 2019, 2:08 p.m.