pbmcPlot

<p>This data was generated from data <code>"pbmc"</code> with default
parameter integration pipeline: normalize, selectGenes, scaleNotCenter,
runINMF, runCluster, runUMAP. To minimize the object size distributed with
the package, rawData and scaleData were removed. Genes are downsampled to
the top 50 variable genes, for smaller normData and \(W\) matrix.</p>

datasets

Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.

Yichen Wang

rliger

Linked Inference of Genomic Experimental Relationships

Joshua Welch

Chao Gao

Jialin Liu

Joshua Sodicoff

Velina Kozareva

Evan Macosko

Paul Hoffman

Ilya Korsunsky

Robert Lee

Andrew Robbins

pbmcPlot function

<p>liger object with two datasets named by "ctrl" and
"stim".</p>

Format

liger object of PBMC subsample data with plotting information available — pbmcPlot

liger object of PBMC subsample data with plotting information available

pbmcPlot: liger object of PBMC subsample data with plotting information available

Description

Usage

Arguments

Format

References