list.responses.factor.minimal {netresponse} | R Documentation

## 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 leo.lahti@iki.fi

### References

See citation('netresponse')

[Package netresponse version 1.54.0 Index]