SFpval: Calculate SigFuge p-value

In pkimes/SigFuge: SigFuge

Description

Function for computing significance of clustering p-value. p-value is obtained from sigclust, a simulation based procedure for testing significance of clustering in high dimension low sample size (HDLSS) data.

The SigClust hypothesis test is given:

• H0: data generated from single Gaussian

• H1: data not generated from single Gaussian

Usage

  SFpval(data, normalize = 1, flag = 1)

Arguments

data	a d x n matrix of read counts at d positions for n samples.
normalize	a n x 1 logical vector of flagged samples.
flag	a n x 1 logical vector of samples flagged as low expression. If flag == 1, default low expression cutoffs are applied to data. If flag == 0, no samples are flagged as low expression (equivalent to setting flag = zeros(n,1)).

Value

SFpval returns an object of class sigclust-class. Avaliable slots are described in detail in the sigclust package. Primarily, we make use of @pvalnorm.

Author(s)

Patrick Kimes <[e-mail]>

Examples

data(geneDepth)
SFout <- SFpval(geneDepth, normalize = 1, flag = 1)
SFout@pvalnorm

pkimes/SigFuge documentation built on May 25, 2019, 8:19 a.m.