fetchData: Fetch Data Functions

In roryk/bcbioSinglecell: Single-Cell RNA-Seq Utilities

Description

Fetch Data Functions

Usage

fetchGeneData(object, ...)

fetchPCAData(object, ...)

fetchTSNEData(object, ...)

fetchTSNEExpressionData(object, ...)

fetchUMAPData(object, ...)

fetchUMAPExpressionData(object, ...)

## S4 method for signature 'SingleCellExperiment'
fetchGeneData(object, genes)

## S4 method for signature 'seurat'
fetchGeneData(object, genes)

## S4 method for signature 'SingleCellExperiment'
fetchPCAData(object, minimal = FALSE)

## S4 method for signature 'seurat'
fetchPCAData(object, minimal = FALSE)

## S4 method for signature 'SingleCellExperiment'
fetchTSNEData(object, minimal = FALSE)

## S4 method for signature 'seurat'
fetchTSNEData(object, minimal = FALSE)

## S4 method for signature 'SingleCellExperiment'
fetchTSNEExpressionData(object, genes)

## S4 method for signature 'seurat'
fetchTSNEExpressionData(object, genes)

## S4 method for signature 'SingleCellExperiment'
fetchUMAPData(object, minimal = FALSE)

## S4 method for signature 'seurat'
fetchUMAPData(object, minimal = FALSE)

## S4 method for signature 'SingleCellExperiment'
fetchUMAPExpressionData(object, genes)

## S4 method for signature 'seurat'
fetchUMAPExpressionData(object, genes)

Arguments

object	Object.
...	Additional arguments.
genes	Gene identifiers. Must match the rownames of the object.
minimal	Return minimal data without metrics.

Value

• fetchGeneData(): matrix.

• fetchTSNEExpressionData(): data.frame containing t-SNE coordinates, sample metadata, and aggregate marker expression values (mean, median, and sum).

• Other functions: data.frame, containing metrics.

Author(s)

Michael Steinbaugh, Rory Kirchner

See Also

Other Data Functions: aggregateReplicates, cell2sample, mapCellsToSamples, metricsPerSample, sampleData, selectSamples, subsetPerSample, topBarcodes

Examples

# SingleCellExperiment ====
object <- indrops_small
genes <- head(rownames(object))

# fetchGeneData
x <- fetchGeneData(object, genes = genes)
glimpse(x)

# seurat ====
object <- seurat_small
genes <- head(rownames(object))

# t-SNE
x <- fetchTSNEData(object)
glimpse(x)

# PCA
x <- fetchPCAData(object)
glimpse(x)

# UMAP
x <- fetchUMAPData(object)
glimpse(x)

# t-SNE gene expression
x <- fetchTSNEExpressionData(seurat_small, genes = genes)
glimpse(x)

# UMAP gene expession
genes <- head(rownames(seurat_small))
x <- fetchUMAPExpressionData(seurat_small, genes = genes)
glimpse(x)

roryk/bcbioSinglecell documentation built on May 27, 2019, 10:44 p.m.