estK: Estimate a value of k to use with RUV

In biobenkj/ATACseeker: Utilities for ATACseq QC, differential accessibility, and integration

Description

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

Usage

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 May 7, 2019, 8:36 a.m.