odds2of3: Odds of passing 2 out of 3 Comparisons

In genejockey33000/typGumbo: Scripts and Pipelines for RNAseq Analysis

Odds of passing 2 out of 3 Comparisons

Description

Highly specialized function to compare whether a set of values in matrix y, are significantly correlated (uncorrected pVal) to 2 out of the 3 columns of values supplied in matrix x. Runs through each column in y and correlates with each of the columns in x then runs a set of tests to determine if correlation passes set rval (set to .35), that rvalue signs agree, and finally that 2 out of the 3 pvals exceed the cutoff (p.cutoff). Subsequently runs a NULL distribution analysis to determine how frequently the observed number of passers would be expected to occur by chance (FDR)

Usage

odds2of3(x, y, method = "pearson", iter = 100, p.cutoff = 0.05, pct = 1)

Arguments

x	matrix of 3 columns to compare (could make this extensible but haven't yet)
y	matrix of expression values (or proteomics or anything really)
method	correlation method to use "spearman", "pearson"
iter	number of iterations (can get slow if too large)
p.cutoff	p value cutoff for determining significance
pct	pct of upper variance to include in comparisons (default = 1 or include all)

genejockey33000/typGumbo documentation built on July 20, 2023, 11:45 p.m.