fsce_small: An example FunctionalSingleCellExperiment

In hesselberthlab/scrunchy: Single Cell Reconstruction of Functional Heterogeneity

Description

Contains sample data for a functional single-cell experiment.

Usage

fsce_small

Format

An object of class FunctionalSingleCellExperiment of length 2.

Details

There are two SingleCellExperiments:

1. rnaseq: a SingleCellExperiment object containing a single-cell mRNA sequencing (10x Genomics V2 3 prime) cell/gene counts matrix in the counts slot. Log-normalized counts are in the logcounts slot.

2. haircut: a SingleCellExperiment object containing a Haircut experiment using DNA repair oligos. Counts are in the counts slot, and centered log-ratio normalized counts are in the logcounts slot.

Haircut repair substrates include:

• A "normal" DNA oligo (Normal_)

• a ribonucleotide (rG) at position 45 (Ribo_)

• an Abasic site at position 45 (Abasic_)

• a uracil:adenosine base-pair, with uracil at position 45 (Uracil_)

• a uracil:guanosine base-pair, with uracil at position 45 (GU_)

Dimensionality reduction calculations are in the rnaseq experiment, including PCA, UMAP, and TSNE slots. In addition, clusters determined by cluster_kmeans() and cluster_leiden() are available as colData.

Source

Generated by data-raw/fsce_small.R.

Examples

fsce_small

# Individual experiments
fsce_small[["rnaseq"]]

fsce_small[["haircut"]]

# Gene and activity names (first 5 items)
rownames(fsce_small[["rnaseq"]])[1:5]

rownames(fsce_small[["haircut"]])[1:5]

# subset with `[` using `[features, cell_ids, experiments]`
features <- c("Uracil_45", "TP53")
cell_ids <- c("TGCGGGTGTAGAGTGC", "CTACGTCCACCACGTG")

fsce_small[features, cell_ids, ]

# dimensionality reduction results
SingleCellExperiment::reducedDimNames(fsce_small[["rnaseq"]])

# UMAP results (first 5 rows)
SingleCellExperiment::reducedDim(fsce_small[["rnaseq"]], "UMAP")[1:5, ]

# k-means cluster IDs
SingleCellExperiment::colData(fsce_small[["rnaseq"]])

hesselberthlab/scrunchy documentation built on Nov. 11, 2019, 2:29 p.m.