list.responses.factor: List significant responses

View source: R/list.responses.factor.R

list.responses.factorR Documentation

List significant responses

Description

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

Usage

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

Arguments

annotation.df

annotation data.frame with discrete factor levels, rows named by the samples

models

List of models. 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

qth

q-value threshold

verbose

verbose

data

data (samples x features; or a vector in univariate case)

rounding

rounding digits

Value

Table listing all associations between the factor levels and responses

Author(s)

Contact: Leo Lahti leo.lahti@iki.fi

References

See citation('netresponse')


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