fitBmeaBatch: Fit the BMEA model for a single batch of units
In steveped/BMEA: Bayesian Modelling for Exon Arrays

Description Usage Arguments Details Value See Also

Fits the BMEA model sequentially for more than one unit

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fitBmeaBatch(celSet, bgCelSet, units, conditions, contMatrix, ...,
  paramToSave = c("c", "mu", "phi"), keepSims = FALSE, zGene = 4.265,
  zExon = 1.645)

`celSet`	an `AffymetrixCelSet` with the data to be fit
`bgCelSet`	a list with components `$lambda` & `$delta`. Each of these must be an `AffymetrixCelSet` containing the means & standard deviations for the background signal priors
`units`	the units (i.e. genes) to be fit
`conditions`	a vector of factors specifying which cell-type/condition each array in the `celSet` belongs to
`contMatrix`	a contrast matrix for the summarised output
`...`	used for passing further arguments such as `mcmcParam` to `runMCMC.BMEA`
`paramToSave`	the model parameters to be saved for downstream processing. The parameters "c", "mu" & "phi" will always be saved.
`keepSims`	logical variable. If `TRUE` all sims from the process & contrasts will be kept
`zGene`	the zScore below which a gene is classified as not detectable above background
`zExon`	the zScore below which an exon is classified as not detectable above background

This is the function used to fit the BMEA model to a batch of units (or genes). Each unit is tested to see if it contains multiple exons, and is expressed detectably above background before analysis. For single exon genes, all exon-level terms are omitted from the model, as the PLM model used for conventional 3' Arrays holds for these genes & can be used with minimal computational effort.

Units that are not fitted are also removed from the output vector of units.

Restricting the parameters to be saved, via the paramToSave argument can significantly save the memory requirements for large batches of genes. This will default to the parameters "c", "mu" & "phi". The signal parameter "S" is the most demanding on memory resources & is generally not advised to be saved unless it is of specific interest.

An object of class("BMEA.Batch"), which is a list with the following components:

$celSet the celSet being analysed, as supplied to the function
$summaries a list with a component for each unit. Each component contains the summary statistics for the unit, including the convergence statistics "rHat" & "nEff."
$logFC a list with a component for each contrast supplied in contMatrix. Each row contains the summary statistics for a single unit, for that contrast
$phiLogFC a list with a component for each contrast supplied in contMatrix. Each row represents an exon (group).
$conditions the cell-types (or conditions) as factors, as supplied to the function
$units a data.frame with the units fit & the corresponding unitNames.
$paramToSave the parameters requested to be saved.
$sims a list with a component for each unit. If keepSims=FALSE, will return NULL for each component.