numCores not working

[andrewelamb]

Hi Dave, I'm using this commit: 30e6215

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]

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]

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]

Oh! I need to rebuild the docs!