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

Description Usage Arguments Value Author(s) References

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

Description

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

Usage

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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 leo.lahti@iki.fi

References

See citation('netresponse')


netresponse documentation built on Nov. 8, 2020, 5:04 p.m.