cellPopT: Assign cell population using correlation

In mchikina/CellCODE: Cell type COmputational Differential Estimation.

Usage

cellPopT(data, grp, SPVs, intCheckPval = 0.1, useAll = F)

Arguments

data	Gene expression data
grp	Clinical group factors.
SPVs	A matrix of cell proportion variables with a row for each sample of data and a column for each cell type.
intCheckPval	P-value for interaction terms that do not match the direction of the group effect. If the interaction is bellow this p-value the gene cell population combination will receive a score of 0. Can be set to 1 do not do any interaction checking.
useAll	Fit a interaction model using all other SPVs as covariates. Not recommended for smaller sample sizes.

Value

A gene by cell-type matrix of scores. Scores are interaction T statistics in absolute value (with some possibly zeroed out).

mchikina/CellCODE documentation built on May 23, 2019, 1:13 p.m.