estK: Estimate a value of k to use with RUV

Description Usage Arguments Value

View source: R/estK.R

Description

This function is used to estimate a suitable value of k for use in RUV normalization

Usage

1
estK(dat, mod, method = "leek", vfilter = NULL, B = 20, seed = 777)

Arguments

dat

A data matrix where loci are rows and samples are columns

mod

A model matrix used to fit the data (variables of interest)

method

The method used to estimate k ("leek" (default - asymptotic) or "be" (permutation-based))

vfilter

Specify the number of loci to filter based on ranked variance across samples (default is to use all loci)

B

Specify the number of permutations to use if method = "be" (default = 20)

seed

Specify a random number for setting the seed if method = "be"

Value

An estimated value of k for using in RUVseq


biobenkj/ATACseeker documentation built on Oct. 8, 2018, 11:11 a.m.