dot-evalDiffCorr: Internal .evalDiffCorr

In GabrielHoffman/decorate: Differential Epigenetic Coregulation Test

Internal .evalDiffCorr

Description

Internal .evalDiffCorr

Usage

.evalDiffCorr(
  epiSignal,
  testVariable,
  gRanges,
  clustList,
  npermute = c(100, 10000, 1e+05),
  adj.beta = 0,
  rho = 0,
  sumabs.seq = 1,
  BPPARAM = bpparam(),
  method = c("sLED", "Box", "Box.permute", "Steiger.fisher", "Steiger", "Jennrich",
    "Factor", "Mann.Whitney", "Kruskal.Wallis", "Cai.max", "Chang.maxBoot", "LC.U",
    "WL.randProj", "Schott.Frob", "Delaneau", "deltaSLE"),
  method.corr = c("pearson", "kendall", "spearman")
)

Arguments

epiSignal	matrix or EList of epigentic signal. Rows are features and columns are samples
testVariable	factor indicating two subsets of the samples to compare
gRanges	GenomciRanges corresponding to the rows of epiSignal
clustList	list of cluster assignments
npermute	array of two entries with min and max number of permutations
adj.beta	parameter for sLED
rho	a large positive constant such that A(X)-A(Y)+diag(rep(rho,p)) is positive definite. Where p is the number of features
sumabs.seq	sparsity parameter
BPPARAM	parameters for parallel evaluation
method	"sLED", "Box", "Box.permute", "Steiger.fisher", "Steiger", "Jennrich", "Factor", "Mann.Whitney", "Kruskal.Wallis", "Cai.max", "Chang.maxBoot", "LC.U", "WL.randProj", "Schott.Frob", "Delaneau", "deltaSLE"
method.corr	Specify type of correlation: "pearson", "kendall", "spearman"

Value

list of result by chromosome and clustList

GabrielHoffman/decorate documentation built on May 23, 2023, 1:29 a.m.