DropoutSimulation: The DropoutSimulation class

In hkumar6/gene.expression: Imputing dropouts in gene expression

Description

This class has slots to store results of different simulations using Lasso and kknn methods.

Simulations on genes with dependency on cells

Simulations on cells with dependency on genes

This function plots the observed v/s predicted values for gene imputation.

This function plots graphs to help analyse between lasso and knn approaches for cell-based imputation.

This function plots graphs to help analyse between lasso and knn approaches for gene-based imputation.

Usage

simulateDropoutGene(theObject, expressionData, dropoutPercentage, n)

## S4 method for signature 'DropoutSimulation'
simulateDropoutGene(theObject, expressionData,
  dropoutPercentage, n)

simulateDropoutCells(theObject, expressionData, dropoutPercentage, n)

## S4 method for signature 'DropoutSimulation'
simulateDropoutCells(theObject, expressionData,
  dropoutPercentage, n)

plot.predict.gene(expressionData, drop.percent, geneID)

## S4 method for signature 'ANY'
plot.predict.gene(expressionData, drop.percent, geneID)

plot.cells(theObject, type = "compare", p = 0)

## S4 method for signature 'DropoutSimulation'
plot.cells(theObject, type = "compare", p = 0)

plot.genes(theObject, type = "compare", p = 0, ...)

## S4 method for signature 'DropoutSimulation'
plot.genes(theObject, type = "compare", p = 0,
  originalData = NULL, methodAttr = NULL)

Arguments

theObject	an object of the DropoutSimulation class
expressionData	the data matrix containing gene expression values, genes as rows and cells as columns
dropoutPercentage	a vector specifying dropout percentages to simulate
n	the number of simulations for each dropout
geneID	the geneID to plot
type	the type of graph to plot, "compare" will plot difference of mse(also the default value)
p	the dropout percentage to plot, default: 0 will consider the whole range
theObject	an object of the DropoutSimulation class
expressionData	the data matrix containing gene expression values, genes as rows and cells as columns
dropoutPercentage	a vector specifying dropout percentages to simulate
n	the number of simulations for each dropout
expressionData	the data of gene expression values
theObject	an object of the DropoutSimulation class containing simulation results
theObject	an object of the DropoutSimulation class containing simulation results
type	the type of graph to plot, "compare" will plot difference of mse(also the default value)
p	the dropout percentage to plot, default: 0 will consider the whole range

Slots

dropout.percentage

Vector containing values between 0 and 1 representing the percentages of dropout to simulate over repitions

n

an integer specifying the number of repititions for a particular dropout percentage

simulation.result.genes

a list storing results of all simulations where genes are imputed as function of cells

simulation.result.cells

a list storing results of all simulations where cells are imputed as functions of genes

hkumar6/gene.expression documentation built on May 17, 2019, 4:33 p.m.