rliger (version 2.0.1)

calcDatasetSpecificity: Calculate a dataset-specificity score for each factor

Description

This score represents the relative magnitude of the dataset-specific components of each factor's gene loadings compared to the shared components for two datasets. First, for each dataset we calculate the norm of the sum of each factor's shared loadings (\(W\)) and dataset-specific loadings (\(V\)). We then determine the ratio of these two values and subtract from 1... TODO: finish description.

Usage

calcDatasetSpecificity(
  object,
  dataset1,
  dataset2,
  doPlot = FALSE,
  do.plot = doPlot
)

Value

List containing three elements.

pct1

Vector of the norm of each metagene factor for dataset1.

pct2

Vector of the norm of each metagene factor for dataset2.

pctSpec

Vector of dataset specificity scores.

Arguments

object

liger object with factorization results.

dataset1

Name of first dataset. Required.

dataset2

Name of second dataset. Required.

doPlot

Logical. Whether to display a barplot of dataset specificity scores (by factor). Default FALSE.

do.plot

Deprecated. Use doPlot instead.