SFpval: Calculate SigFuge p-value

Description Usage Arguments Value Author(s) Examples

View source: R/SFpval.R

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:

Usage

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  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 <pkimes@live.unc.edu>

Examples

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

SigFuge documentation built on Nov. 8, 2020, 6:17 p.m.