coseqResults: coseqResults object and constructor

In coseq: Co-Expression Analysis of Sequencing Data

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

coseq documentation built on Nov. 8, 2020, 5:18 p.m.