DoMetaEfron: An R-function to perform a meta-analysis over multiple...

In EpiDISH: Epigenetic Dissection of Intra-Sample-Heterogeneity

Description

An R-function to perform a meta-analysis over multiple studies using an empirical Bayes procedure by Efron followed by Stouffer method.

Usage

DoMetaEfron(stat.m, pval.m, bre = 120, df = 15, pct0 = 0.25, plotlocfdr = 0)

Arguments

stat.m	A matrix of signed statistics (e.g. t-statistics) with rows labeling genomic features (e.g. CpGs or genes) and columns labeling studies. rownames must be provided.
pval.m	A matrix matched to stat.m containing the associated P-values, with rows labeling genomic features (e.g. CpGs or genes) and columns labeling studies.
bre	The number of breakpoints to divide statistics per study into bins. By default this is 120. See input argument for locfdr function from locfdr package.
df	The number of degrees of freedom for fitting spline. By default this is 15. See input argument for locfdr function from locfdr package.
pct0	Percentage of statistics to use for fitting null. By default this is 0.25 (i.e. 25%).
plotlocfdr	Determines whether to plot output or not. By default this is set to 0 meaning no plot. See input argument for locfdr function from locfdr package.

Value

meta.m A matrix with rows as in stat.m, and with 3 columns labeling Stouffer's z-statistic, P-value and Benjamini-Hochberg adjusted P-value.

EpiDISH documentation built on Nov. 8, 2020, 6:52 p.m.