geva.quick {geva} | R Documentation |
Given a GEVAInput
object, applies the geva.summarize()
, geva.quantiles
, geva.cluster
, and geva.finalize
in a single call. Optional arguments are passed to the internal calls of these functions.
geva.quick(gobject, ...)
gobject |
A |
... |
Optional arguments passed to |
This function performs the summarization, quantile detecetion, and clustering of an input data, then merges the results together and, if applicable, performs a factor analysis. If the gobject
is not a GEVAInput
, it must provide a valid GEVAInput
object when called by inputdata(gobject)
. Moreover, all parameters used in previous analysis will be taken into account. For instance, if gobject
is a GEVASummary
obtained by using variation.method='mad'
, the internal call to geva.summarize
in this function will use variation.method='mad'
as well, unless if another parameter for variation.method
is specified in the ...
arguments.
Therefore, this function can be useful not only as a shortcut to analyze GEVAInput
but also for parameter testing when applied to a GEVAResults
object, since the previous parameters are reused, while the specified parameters are overriden.
A GEVAResults
object
## Basic usage using a random generated input ginput <- geva.ideal.example() # Generates a random input example gresults <- geva.quick(ginput) # Performs the entire analysis (default parameters) print(head(top.genes(gresults))) # Prints the results plot(gresults) # Plots the final SV-plot ## Example with non-default parameters ginput <- geva.ideal.example() # Generates a random input example gresults <- geva.quick(ginput, summary.method="median", variation.method="mad", quantiles.method="density", cluster.method="density", resolution=0.32) print(head(top.genes(gresults))) # Prints the results plot(gresults) # Plots the final SV-plot