Tempora-class: Define a class of Tempora object

In BaderLab/Tempora: Pathway-based Trajectory Inference for Time-series Single Cell RNA-Seq Data

Description

A Tempora object contains the input gene expression matrix and metadata, as well as stores the meta data of each cluster, the clusters' pathway enrichment profiles, the constructed trajectory as well as the Sugiyama layout for the trajectory plot

Usage

data(x)

data(x) <- value

## S4 method for signature 'Tempora'
data(x)

## S4 replacement method for signature 'Tempora'
data(x) <- value

meta.data(x)

meta.data(x) <- value

## S4 method for signature 'Tempora'
meta.data(x)

## S4 replacement method for signature 'Tempora'
meta.data(x) <- value

cluster.metadata(x)

cluster.metadata(x) <- value

## S4 method for signature 'Tempora'
cluster.metadata(x)

## S4 replacement method for signature 'Tempora'
cluster.metadata(x) <- value

cluster.pathways(x)

cluster.pathways(x) <- value

## S4 method for signature 'Tempora'
cluster.pathways(x)

## S4 replacement method for signature 'Tempora'
cluster.pathways(x) <- value

cluster.pathways.dr(x)

cluster.pathways.dr(x) <- value

## S4 method for signature 'Tempora'
cluster.pathways.dr(x)

## S4 replacement method for signature 'Tempora'
cluster.pathways.dr(x) <- value

varying.pws(x)

varying.pws(x) <- value

## S4 method for signature 'Tempora'
varying.pws(x)

## S4 replacement method for signature 'Tempora'
varying.pws(x) <- value

gams(x)

gams(x) <- value

## S4 method for signature 'Tempora'
gams(x)

## S4 replacement method for signature 'Tempora'
gams(x) <- value

n.pcs(x)

n.pcs(x) <- value

## S4 method for signature 'Tempora'
n.pcs(x)

## S4 replacement method for signature 'Tempora'
n.pcs(x) <- value

trajectory(x)

trajectory(x) <- value

## S4 method for signature 'Tempora'
trajectory(x)

## S4 replacement method for signature 'Tempora'
trajectory(x) <- value

layouts(x)

layouts(x) <- value

## S4 method for signature 'Tempora'
layouts(x)

## S4 replacement method for signature 'Tempora'
layouts(x) <- value

Arguments

x	Tempora object
value	New value

Slots

data

A gene expression matrix (genes x cells), often aggregated from multiple time points

meta.data

A dataframe containing the metadata for the cells in the gene expression matrix, which at minimum includes the collection timepoint and cluster identity of each cell

cluster.metadata

A dataframe containing the metadata for each cell cluster

cluster.pathways

A dataframe containing the pathway enrichment profile of each cluster as calculated by CalculatePWProfiles

cluster.pathways.dr

A prcomp object containing the PCA of the clusters' pathway enrichment profiles

n.pcs

The number of principal components to be used in trajectory construction

trajectory

A dataframe describing the inferred trajectory as inferred by BuildTrajectory

layouts

A matrix containing the Sugiyama layout of the trajectory to be used in PlotTrajectory

varying.pws

A list of temporally varying pathways identified by IdentifyVaryingPWs

BaderLab/Tempora documentation built on April 25, 2021, 2:10 p.m.