fetchData: Fetch Data Functions

Description Usage Arguments Value Author(s) See Also Examples

Description

Fetch Data Functions

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
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

Author(s)

Michael Steinbaugh, Rory Kirchner

See Also

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

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
# 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.