PCA: Dimension Reduction.

In bioinfoDZ/RISC: Robust Integration of Single-Cell RNA-Seq Datasets

Dimension Reduction.

Description

Based on highly variably expressed genes of the datasets, RISC calculates the principal components (PCs) of the cells using prcomp functions. The major PCs, which explain most gene expression variance, are used for dimension reduciton.

Usage

scPCA(object, npc = 20)

Arguments

object	RISC object: a framework dataset.
npc	The number of PCs will be generated based on highly variable genes (usually < 1,500), npc equal to the first 20 PCs as the default.

Value

RISC single cell dataset, the DimReduction slot.

References

Jolliffe et al. (2016)

Alter et al., PNAS (2000)

Gonzalez et al., JSS (2008)

Mevik et al., JSS (2007)

Examples

# RISC object
obj0 = raw.mat[[3]]
obj0 = scPCA(obj0, npc = 10)

bioinfoDZ/RISC documentation built on March 30, 2024, 9:19 p.m.