subRM: Trim the incidence matrix

In wiscstatman/Rolemodel: Gene-set analysis via MFA

Description

Trim the incidence matrix using two parameters n.low and n.up.

Usage

subRM(I, n.low, n.up)

Arguments

I	The incidence 0-1 matrix with unique row and column names, where rows are parts (genes) and columns are wholes (gene-sets).
n.low	The lower bound of the sums of columns in the incidence matrix.
n.up	The upper bound of the sums of columns in the incidence matrix.

Details

Trim the size of the incidence matrix for the computation via integer linear programming (ILP). The suggested values are n.low = 5 and n.up = 50.

Value

Return the new incidence matrix after trimming.

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)
## Use 5 and 10 as the trimming parameters
## newI <- subRM(t2d$I, 5, 10)

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