library_sizes {linear} R Documentation

Get the implied library size of every training sample of the fitted network.

Description

Usage

library_sizes(model,
    pseudo = 1);

Arguments

model

the perturbation engine that is created via elastic_model. [as ElasticNet]

pseudo

the pseudo count offset that was used by the log transformation, default 1. [as double]

Details

This vector is the bridge between an external raw count matrix and the model space: normalize the counts with y = counts / sum(counts) * median(library_sizes) and then apply x = log2(y + pseudo).

Authors

TRNtoolkit

Value

a numeric vector, one value per training sample, i.e. sum(2^x - pseudo) of the expression matrix that was used to fit the network.

clr value class

Examples

[Package linear version 1.0.0.0 Index]