do.permutations: do.permutations

In ERGlass/lrcde.dev: Linear Regression Cell Type-Specific Differential Expression Power Analysis

Description

Called from sim_driver_script.

Usage

do.permutations(het, cell.props, groups, nperms = 100, medCntr, stdz, nonNeg)

Arguments

het	Should be samples by genomic site (rows by columns). The samples by genomic measures heterogeneous observations matrix.
cell.props	Should be samples by cell types (rows by columns). The relative cell proportions per sample.
groups	A vector of 1's and 2's indicating group membership per sample. Should align with samples in het.sub and cell.props.
nperms	Integer value indicating number of group label permutations to perform when simulating each site's parameters.
medCntr	Boolean indicating whether to median center differential expression estimates.
stdz	Boolean indicating whether to 'standardize' differential expression estimates.
nonNeg	Boolean indicating whether to force cell type-specific expression estiamtes to be non-negative.

Value

An 3-dimensional array of cell type-specific differential expression estimates for each permutation by each cell type by each genomic site.

Author(s)

Edmund R Glass, [e-mail]

References

https://github.com/ERGlass/ERGmisc

Examples

do.permutations( het.obs, cell.props, groups, n.perms=1000,  medCntr, stdz, nonNeg )

ERGlass/lrcde.dev documentation built on May 6, 2019, 3:09 p.m.