coseqResults: coseqResults object and constructor

Description Usage Arguments Details Value

View source: R/aaa-AllClasses.R

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

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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


andreamrau/coseq documentation built on July 25, 2021, 10:17 a.m.