combine.pvalue: combine.pvalue

In xinchoubiology/Rcppsva: Rcpp Integration Surrogate Variable Analysis

Description

combine-pvalue accepts a list of pvalues of probes, and correlation matrices are claculated by input data matrix. Then, it estimate combined pvalue for candidate regions defined in input region list

Usage

combine.pvalue(dat.m = NULL, pvalues, cluster, chr, pos, names,
  method = c("spearman", "pearson", "kendall"),
  combine = c("stouffer_liptak", "zscore"), weight = NULL, cutoff = 0.1,
  cores = detectCores())

Arguments

dat.m	n x m delta M|beta matrix for n CpG sites across 2*m paired different patient samples
pvalues	pvalue column vector for each probe
cluster	correlated cluster list calculated by corrclusterMaker cluster list contains: single probe cluster, multiple probes cluster
chr	chromosome vector
pos	position vector
names	probe names vector ; used in function clusterMaker
method	correlation calculation method; c("spearman", "pearson", "kendall"); Default "spearman"
combine	combine pvalue method; c("stouffer_liptak", "zscore")
weight	NULL; weight provided as 1/sigma of each probe. It means each probe's contribution to defined regions
cutoff	cutoff for dmr(differential methylated regions) detection's qvalue(fdr); Default 0.1
cores	core number for R backend combp algorithm

Details

calculation combination pvalue of given regions(pvalues within region are correlated)

Value

combine-pval

xinchoubiology/Rcppsva documentation built on May 4, 2019, 1:06 p.m.