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mani2012 / PathoStat

The purpose of this package is to perform Statistical Analysis on the PathoScope generated reports files.
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Accommodate phyloseq-class objects throughout #5

Closed tfaits closed 8 years ago

tfaits commented 8 years ago

Currently, PathoStat takes a data matrix, batch information, and condition information as inputs, and is limited to those options. Instead, we're going to coerce any input (PathoScope report, .biom files, etc) into a phyloseq-class object, and pass that object along. This allows for the user to attach any number of covariates or phenotypic data along with the data matrix. This also means a general overhaul of almost every function in the package.

mani2012 commented 8 years ago

Added new feature with a new PathoStat class that extends the phyloseq class. Added a simplified entry function runPathoStat that takes the pathostat object as the input. The pathostat object extends phyloseq and has all the information loaded now, including the full sample data information.