mergeNodes: Merge the CEL files written on multiple nodes into a single...
In steveped/BMEA: Bayesian Modelling for Exon Arrays

Description Usage Arguments Details Value See Also

Takes the node specific sets of CEL files containing BMEA contrast & model parameter data and merges them into a single set of CEL files.

1 2	mergeNodes(celSet, nodePaths, outDir = NULL, ..., paramToWrite = NULL, nodeUnits = NULL, visible = FALSE, verbose = TRUE)

`celSet`	the parent celSet being analysed
`nodePaths`	where to find all the node specific CEL files
`outDir`	the directory to merge the node-level information to.
`...`	not used
`paramToWrite`	the model parameters to collect from each node & write to the merged CEL files
`nodeUnits`	a `list` with a vector of units for each node that correspond to those processed on each node. Overrides any information contained in the log files. The units will be extracted from the log files if this is not supplied
`visible`	if `visible=TRUE` a `list` will be returned, otherwise the function will invisibly return `TRUE`. Defaults to FALSE
`verbose`	determines the amount of information to display. Defaults to `TRUE`

During analysis using parallel nodes, each node will write to a batch of CEL files in its own separate directory. This function collects the units that have been run on each node and copies the saved results from the CEL files on each node to a main set of CEL files in the root directory.

CEL files with the contrast data (i.e. logFC & phiLogFC) will be written to the directories bmeaData/contrastData/parentName,logFC/chipType & bmeaData/contrastData/parentName,phiLogFC/chipType respectively. If no output directory is set via outDir the current working directory will be used.

CEL files with model parameters will be written to the directories bmeaData/modelData/parentName,parameterName/chipType.

If visible=FALSE will invisibly return TRUE, otherwise a list will be returned with the following elements:

$written TRUE
$parameters contains the model parameters that have been written to the set of CEL files.
$nodeUnits the units processed on each node
$nodePaths the paths the node specific CEL files were sourced from
$logFiles the contents of the log files from each node

AffymetrixCelSet

steveped/BMEA documentation built on May 30, 2019, 5:38 p.m.