list.responses.factor.minimal: List factor responses (minimal)

In antagomir/netresponse: Functional Network Analysis

List factor responses (minimal)

Description

List significantly associated responses for all factors and levels in the given annotation matrix

Usage

list.responses.factor.minimal(
  annotation.df,
  groupings,
  method = "hypergeometric",
  min.size = 2,
  pth = Inf,
  verbose = TRUE,
  data = NULL,
  rounding = NULL
)

Arguments

annotation.df	annotation data.frame with discrete factor levels, rows named by the samples
groupings	List of groupings. Each model should have a sample-cluster assignment matrix qofz, or a vector of cluster indices named by the samples.
method	method for enrichment calculation
min.size	minimum sample size for a response
pth	p-value threshold; applied to adjusted p-value
verbose	verbose
data	data (samples x features; or a vector in univariate case)
rounding	rounding digits

Value

A list with two elements: Table listing all associations between the factor levels and responses; multiple p-value adjustment method

Author(s)

Contact: Leo Lahti [e-mail]

References

See citation('netresponse')

antagomir/netresponse documentation built on March 30, 2023, 7:24 a.m.