scalpel (version 1.0.3)

getScalpelStep2: Read in results from Step 2 of SCALPEL.

Description

This step allows the user to retrieve the object of class scalpelStep2 for results from a previous session.

Usage

getScalpelStep2(outputFolder, version = NULL, cutoff = 0.18, omega = 0.2)

Arguments

outputFolder

The existing directory where the results that the user wishes to use are saved.

version

The 5-digit folder ID for the results that the user wishes to load. If NULL, automatically chooses the only version in outputFolder and if more than one version exists, returns an error.

cutoff

A value in [0,1] indicating the dendrogram cutpoint used. The default value is 0.18.

omega

A value in [0,1] indicating the dissimilarity metric weight used for clustering. The default value is 0.2.

Value

An object of class scalpelStep2, which can be used to run SCALPEL Step 3 using scalpelStep3 or can be used with the plotting functions plotCluster and plotSpatial.

See Also

scalpelStep2, scalpel

Examples

# NOT RUN {
### many of the functions in this package are interconnected so the
### easiest way to learn to use the package is by working through the vignette,
### which is available at ajpete.com/software

#assumes you have run the example for the "scalpel" function
#folder where results were saved
outputFolder = "scalpelResults"

#read previous results in
#simplest example with default parameters:
out = getScalpelStep2(outputFolder = outputFolder)
#note: if Step 1 has been run more than once, will need to specify 'version'

#example with optional parameters:
#need to enter if non-default options were used
out = getScalpelStep2(outputFolder = outputFolder, omega = 0.2, cutoff = 0.18)
# }