mds-methods: Calculate MDS projections for the 3D Make3Dobj function

In stela2502/BioData: The package allows to annotate a numeric data.table with col and row data

Description

Calculates the MDS for a given MDS type and stores the 3 dimensions in the object for later use. All projections use a n=100 PCA projection as starting material instead of the raw data.

Arguments

dataObj	the BioData object
mds.type	Which MDS function should be called default="PCA"
onwhat	condense which dataset at the moment only Expression is supported default='expression'
genes	do it on genes not on samples (default = F)
LLEK	the neighbours in the LLE algorithm (default=2)
useRaw	base the projection on the raw data and not the n=100 PCA data (default FALSE)
pythonEnv	if needed the virtual environment for the MulticoreTSNE call set to something like 'source <myPrivateEnvPath>/bin/activate' (default = NULL)
dim	the number of dimensions to return ( default 3)

stela2502/BioData documentation built on Feb. 23, 2022, 5:47 a.m.