regionSeeker: regionSeeker

In xinchoubiology/Rcppsva: Rcpp Integration Surrogate Variable Analysis

Description

bump hunting algorithm one clusters predefined by distance/correlation constraints

Usage

regionSeeker(beta, chr, pos, cluster = NULL, maxGap = 500, names,
  pvalc = 0.1, cutoff = c(quantile(abs(beta), 1 - pvalc),
  quantile(abs(beta), pvalc)), permbeta = NULL, mcores = 2, corr = FALSE,
  qvalue = 0.1, drop = FALSE, verbose = FALSE)

Arguments

beta	vector of different probes
chr	Chromosome vector
pos	position numeric vector
cluster	list clusters defined by arguments or clusterMaker
maxGap	max gap length between 2 probes within a region ; used in function clusterMaker
names	probe names vector ; used in function clusterMaker
pvalc	pvalue cutoff for bump selection; Default 0.1
cutoff	cutoff threshold for bump selection. only segements within cluster satisfy cutoff are returned as predicted region c(sig-cutoff, null-cutoff)
permbeta	Null hypothesis beta distribution [added permbeta(H0 distribution) to the end columns of region table from regionSeeker]
mcores	multiple threads used in regionSeeker
corr	logical, whether the cluster is generated under distance constraint or under correlation constraint. Default FALSE
qvalue	cutoff of FDR(false discovery rate)
drop	FALSE; create discriminate table (significant | null) or not
verbose	FALSE

Details

If an arbitary threshold is defined, regionSeeker will return a table (within / without) the threshold. In bump hunting algorithms, these contiguous probes mean bumps.

Value

Table of predict regions

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