TimeSeriesExperiment: Time Series Experiment Class

In nlhuong/TimeSeriesExperiment: Analysis for short time-series data

Description

TimeSeriesExperiment is an extension of SummarizedExperiment class with the following new slots (in addition to SummarizedExperiment slots).

Constructor for 'TimeSeriesExperiment' object which stores same data as SummarizedExperiment but also slots for time, group, replicate and other time-series formated data useful for applyting data-analysis.

Usage

TimeSeriesExperiment(
  ...,
  timepoint = numeric(0),
  group = character(0),
  replicate = character(0)
)

Arguments

...	For SummarizedExperiment:: SummarizedExperiment, S4 methods list and matrix, arguments identical to those of the SimpleList method.
timepoint	a vector indicating timepoint at which each sample was collected or a character string equal to one of the column names of a supplied colData.
group	a vector indicating a group membership for each sample or a character string equal to one of the column names of a supplied colData. If not specified, the group is set to 'G1' for each sample.
replicate	a vector indicating a replicate id of each sample or a character string equal to one of the column names of a supplied colData. If not specified, the replicate is set to 'R1' for each sample.

Details

The TimeSeriesExperiment class is an object (the main data container) used for in the time series/course experiment analysis. It stores all relevant information associated with the dataset, including the raw data, group, replicate and time associated with each sample (column of the data). The object includes also slots for results from some class-specific methods.

TimeSeriesExperiment constructor initializes the TimeSeriesExperiment TimeSeriesExperiment object and populates the time, replicate, and group slots.

Value

Returns an initialized TimeSeriesExperiment object.

Slots

timepoint

A vector indicating the time-point of each sample collection.

group

A vector indicating the group membership of each sample.

replicate

A vector indicating the replicate id of each sample.

assayCollapsed

A matrix with assay data aggregated over replicates.

colDataCollapsed

A DataFrame where rows correspond to samples aggregated over replicates and columns indicate group membership and time-point.

timeSeries

A list of time-course formatted data. Each element of the list is a DataFrame with the first three columns indicating feature, group, replicate, and the remaining ones storing the assay data at consecutive time points. TimeSeriesExperiment methods will typically generate elements of the list named: 'ts', 'ts_collapsed'.

dimensionReduction

A list of results from applying dimmensionality reduction methods; elements named by technique used.

clusterAssignment

A list of results from clustering of the time-series features (rows) containing elements: 'settings', 'hclust', 'clust_map' and 'clust_centroids'.

differentialExpression

A list of results from differential expression analysis. Either from point-wise ('timepoint_de') or trajectory ('trajectory_de') differential expression analysis.

Examples

raw <- matrix(runif(3000), ncol = 30)
timepoint <- rep(rep(1:5, each = 3), 2)
replicate <- rep(1:3, 10)
group <- rep(1:2, each = 15)
test_TimeSeriesExperiment <- TimeSeriesExperiment(
    assays = list(raw),
    timepoint = timepoint,
    replicate = replicate,
    group = group)
test_TimeSeriesExperiment

nlhuong/TimeSeriesExperiment documentation built on Sept. 8, 2021, 12:30 a.m.