DISCBIO: The DISCBIO Class

In DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics

The DISCBIO Class

Description

The DISCBIO class is the central object storing all information generated throughout the pipeline.

Arguments

object

An DISCBIO object.

Details

DISCBIO

Slots

SingleCellExperiment

Representation of the single cell input data, including both cells from regular and ERCC spike-in samples. Data are stored in a SingleCellExperiment object.

expdata

The raw expression data matrix with cells as columns and genes as rows in sparse matrix format. It does not contain ERCC spike-ins.

expdataAll

The raw expression data matrix with cells as columns and genes as rows in sparse matrix format. It can contain ERCC spike-ins.

ndata

Data with expression normalized to one for each cell.

fdata

Filtered data with expression normalized to one for each cell.

distances

A distance matrix.

tsne

A data.frame with coordinates of two-dimensional tsne layout for the K-means clustering.

background

A list storing the polynomial fit for the background model of gene expression variability. It is used for outlier identification.

out

A list storing information on outlier cells used for the prediction of rare cell types.

cpart

A vector containing the final clustering partition computed by K-means.

fcol

A vector contaning the colour scheme for the clusters.

filterpar

A list containing the parameters used for cell and gene filtering based on expression.

clusterpar

A list containing the parameters used for the K-means clustering.

outlierpar

A list containing the parameters used for outlier identification.

kmeans

A list containing the results of running the Clustexp() function.

MBclusters

A vector containing the final clustering partition computed by Model-based clustering.

kordering

A vector containing the Pseudo-time ordering based on k-means clusters.

MBordering

A vector containing the Pseudo-time ordering based on Model-based clusters.

MBtsne

A data.frame with coordinates of two-dimensional tsne layout for the Model-based clustering.

noiseF

A vector containing the gene list resulted from running the noise filtering.

FinalGeneList

A vector containing the final gene list resulted from running the noise filtering or/and the expression filtering.

Examples

class(valuesG1msTest)
G1_reclassified <- DISCBIO(valuesG1msTest)
class(G1_reclassified)
str(G1_reclassified, max.level = 2)
identical(G1_reclassified@expdataAll, valuesG1msTest)

DIscBIO documentation built on Nov. 6, 2023, 5:08 p.m.