coseqResults-class {coseq} | R Documentation

## coseqResults object and constructor

### Description

`coseqResults` is a subclass of `RangedSummarizedExperiment`, used to store the co-expression results as well as some additional information useful for plotting (`tcounts`, `y_profiles`) and meta-information about the co-expression analysis (`transformation`, `normFactors`).

### Usage

    coseqResults(
      SummarizedExperiment,
      allResults,
      model = NULL,
      transformation = NULL,
      tcounts = NULL,
      y_profiles = NULL,
      normFactors = NULL
    )

### Arguments

`SummarizedExperiment` | a `RangedSummarizedExperiment` of `coseq` results
`allResults` | List of conditional probabilities of cluster membership for each gene, in all models fit
`model` | `"Normal"` or `"Poisson"`, the mixture model used for co-expression
`transformation` | Transformation applied to counts to obtain `tcounts`
`tcounts` | Transformed counts used for mixture model fitting
`y_profiles` | y profiles used for `coseq` plotting
`normFactors` | Scaling factors used for normalization

### Details

This constructor function would not typically be used by "end users". This simple class extends the `RangedSummarizedExperiment` class of the SummarizedExperiment package to allow other packages to write methods for results objects from the coseq package. It is used by `coseqRun` to wrap up the results table.

### Value

a coseqResults object

[Package coseq version 1.14.0 Index]