CellMix 1.6

Extracting Expression Data

Description

Extracts expression data (usually as ExpressionSet objects) from other objects.

Usage

eset(object, ...)

S4 (GEDdata_entry)
`eset`(object, load = TRUE, filter = TRUE, verbose = FALSE, save = TRUE, 
  cache = TRUE)

Arguments

object
object from which to extract the expression data
...
extra argument to allow extension. See each method's description for more details,.
load
logical that indicates if the primary data should be (re-)loaded, or a character string giving the path of the file from where to load the data, which will typically be the Matrix file as downloaded from GEO. If FALSE the gene expression data is not loaded and the result will be NULL if the dataset has not already been loaded in a previous call. If explicitly TRUE (i.e. not missing), then the data is (re-)loaded from cache, or downloaded from a public repository if it has not been previously cached. In this case, the pre-processing pipeline is performed again.
filter
logical that indicates if the preprocessing pipeline should be applied to the "plain" data. If TRUE then the processing/filtering function associated with the data (registry field 'filter') is applied. A custom pre-processing function may also be passed. If FALSE, no processing is performed on the data.
verbose
logical/number that toggles verbose messages. To better monitor how the data is generated/processed, it is recommended to toggle on verbosity, and use numeric values at various levels (e.g. verbose=3) to display more detailed outputs.
save
logical that indicates if the data should be saved in in R binary format in the local GED cache, for fast future loading -- possibly in a different R session.
cache
logical that indicates if the data should be retrieved from the local cache if present, or re-(down)loaded. If some remote data has been downloaded by a previous call to eset, these data are generally loaded from disk and not re-downloaded by the relevant package (e.g., GEOquery or ArrayExpress). If save=TRUE (as default), the new data will replace any previously downloaded data.

Value

an ExpressionSet object.

Methods

  1. esetsignature(object = "ExpressionMix"): Extracts an ExpressionSet object from an ExpressionMix object.

    Because ExpressionMix-class inherits from ExpressionSet-class, this methods simply returns the object coerced as an ExpressionSet object.

  2. esetsignature(object = "GEDdata_entry"): Extracting Expression Data from CellMix Dataset Registry Entry.

    Loads and extracts the expression data from a CellMix registry dataset entry, as an ExpressionSet object.

    The first time the expression data is accessed, and if argument load=TRUE, it is loaded from the local storage if possible (cf. GEDsave), or downloaded from GEO using GEDdownload. It is then pre-processed (see below) and the resulting value (an ExpressionSet object) is cached in the GEDdata_entry environment. Subsequent calls use the cached value.

    The data pre-processing consists in filtering and extraction/addition of phenotypic or feature annotation data. The filtering is performed by the function stored in element object$filter. The extra phenotypic data is generated by the function stored in element object$pdata. The extra feature data is generated by the function stored in element object$fdata. Note that the whole pre-processing pipeline is not cached.

Examples


## Not run: 
##D # get data from the registry
##D e <- gedData('GSE20300')
##D # this is an ExpressionMix object
##D e
##D # extract the ExpressionSet part
##D class(eset(e))
## End(Not run)

See also

ExpressionSet