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CRI-iAtlas / ImmuneSubtypeClassifier

An R package for classification of immune subtypes, in cancer, using gene expression data.
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numCores not working #4

Open andrewelamb opened 5 years ago

andrewelamb commented 5 years ago

Hi Dave, I'm using this commit: 30e6215c390bf12761d17cbc9647ac4527e319ba

and getting this error:

calls <- ImmuneSubtypeClassifier::callEnsemble( input_matrix, numCores = args$num_cores )

Error in ImmuneSubtypeClassifier::callEnsemble(input_matrix, numCores = args$num_cores) : unused argument (numCores = args$num_cores) Execution halted

Gibbsdavidl commented 5 years ago

The function signature is:

callEnsemble <- function(X, path='data', geneids='symbol')

Should be able to use defaults for path and geneids..

There's something wrong (I think) with the parallel version unfortunately.

andrewelamb commented 5 years ago

When you do: ?ImmuneSubtypeClassifier::callEnsemble

you get:

callEnsemble {ImmuneSubtypeClassifier} R Documentation callEnsemble Make subtype calls for each sample Description callEnsemble Make subtype calls for each sample

Usage callEnsemble(X, path = "data", geneids = "symbol", numCores = 2) Arguments X
gene expression matrix, genes in row.names, samples in column.names

path
the path to the ensemble model, stored as RData, and named 'ens'

geneids either hgnc for gene symbols or entrez ids. will be matched to the EB++ matrix

numCores
number of cores to use with parallel lib

Value table, column 1 is best call, remaining columns are subtype prediction scores.

Examples calls <- callEnsemble(mods, X, Y)

Gibbsdavidl commented 5 years ago

Oh! I need to rebuild the docs!