oddsratio.pairwise: Calculate pairwise gene odds ratios

In amcdavid/SingleCellAnalysis: Tools for Analysis of Zero-Inflated, Continuous Data

Description

Calculates odds ratios between each pair of genes on the dichotomous level.

Usage

oddsratio.pairwise(sc, Formula, surrenderFreq = 0.05, useFirth = FALSE,
  lm.hook, MAX_IT = 30)

Arguments

sc	SingleCellAssay object
Formula	a formula used to build the design matrix. Probably should include the term 'logOR.primer2' (if the pairwise odds ratios are indeed desired).
surrenderFreq	any pair of genes in which either is expressed above or below this threshold will be skipped
useFirth	should biased-reduced regression be used via brglm. Slow.
lm.hook	a function to be called on the fitted regression
MAX_IT	if useFirth==TRUE, how many iterations should be permitted?

Value

PairwiseOddsRatio class, with slots fits (2-D list of fit) and genes (character vector of gene names).

amcdavid/SingleCellAnalysis documentation built on May 10, 2019, 10:27 a.m.