SCD-class: Single Cell Dataset

In wjawaid/bglab: Berthold Gottgens lab scRNA seq

Description

This is the main class in the bglab package. It stores all the data. Three datatables are required to generate a new object. Both qPCR and RNAseq data may be used.

Slots

useFilter

Logical. To filter dataset or not

filterGene

Logical. To filter genes from dataset or not

filterCell

Logical. To filter cells from dataset or not

pca

Contains a PCA object

diffMap

Contains a DiffusionMap object

tsne

Contains a TSNE object

isomap

Contains a Isomap object

counts

Contains a matrix of raw counts.

spike

Spike-in matrix.

qcCounts

Quality Control matrix.

filterQC

Default TRUE. Will not return cells that failed QC when set to TRUE.

qcOutput

List containing QC output.

technicalNoise

List containing technical noise output. Highly recommended.

wjawaid/bglab documentation built on May 4, 2019, 6:33 a.m.