analysis_examples: BEARscc downstream example objects.

In seversond12/BEARscc: BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)

Description

The analysis_examples Rdata object contains downstream data objects for use in various help pages for dynamic execution resulting from running tutorial in README and vignette on BEARscc_examples. The objects are a result of applying BEARscc functions as described in the README found at https://bitbucket.org/bsblabludwig/bearscc.git or the vignette that accompanies this package.

Usage

data("analysis_examples")

Format

An R data file with:

data.frame	"BEARscc_clusts.df"	Toy dataframe of previously computed cluster labels for each cell across various cluster numbers and the original clustering.
	[,1]	2 cluster case
	[,2]	3 cluster case
	[,3]	4 cluster case
	[,4]	5 cluster case
	[,5]	Original cluster case
data.frame	"clusters.df"	Toy dataframe of previously computed hierarchical clustering of 10 BEARscc simulated technical replicates as described in README and original hierarchical clustering, see recluster below.
	[,1]	Cluster labels from simulated replicate 1.
	[,2]	Cluster labels from simulated replicate 2.
	[,3]	Cluster labels from simulated replicate 3.
	[,4]	Cluster labels from simulated replicate 4.
	[,5]	Cluster labels from simulated replicate 5.
	[,6]	Cluster labels from simulated replicate 6.
	[,7]	Cluster labels from simulated replicate 7.
	[,8]	Cluster labels from simulated replicate 8.
	[,9]	Cluster labels from simulated replicate 9.
	[,10]	Cluster labels from simulated replicate 10.
	[,11]	Original cluster case
function	"recluster"	A function used to quickly illustrate replicate-wise clustering and the resulting consensus aspect of BEARscc. It is utilized in the README.
matrix	"noise_consensus"	50 by 50 matrix of previously computed output from compute_consensus(), which is the noise consensus matrix resulting from the toy dataset, BEARscc_examples.
SCEList	"BEAR_analyzed.sce"	A SingleCellExperiment object discussed extensively in the vignette and ReadME.

Value

An R data file with a function, matrix, two data.frame objects and a SingleCellExperiment object.

Source

These data are the result of running the README, https://bitbucket.org/bsblabludwig/bearscc.git, on a subset of observations obtained by Drs. Michael White and Richard Owen in the Xin Lu Lab. Samples were sequenced by the Wellcome Trust Center for Genomics, Oxford, UK. The original data used to generate these objects are available in full with GEO accession number, GSE95155.

References

Source code and README: <https://bitbucket.org/bsblabludwig/bearscc/overview> Associated preprint: <https://www.biorxiv.org/content/early/2017/06/05/118919>

Examples

data(analysis_examples)

seversond12/BEARscc documentation built on June 8, 2020, 8:04 a.m.