sampleData: Sample Data

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

Description

Metadata in columns describing the samples, which are defined in the rownames. Similar to colData(), which for bcbioSingleCell and SingleCellExperiment objects describes cells in the columns, rather than the samples.

Usage

## S4 method for signature 'SingleCellExperiment'
sampleData(object, interestingGroups,
  clean = TRUE, return = c("DataFrame", "data.frame", "kable"))

## S4 method for signature 'seurat'
sampleData(object, interestingGroups, clean = TRUE,
  return = c("DataFrame", "data.frame", "kable"))

## S4 replacement method for signature 'SingleCellExperiment,DataFrame'
sampleData(object) <- value

## S4 replacement method for signature 'seurat,DataFrame'
sampleData(object) <- value

Arguments

object	Object.
interestingGroups	character. Groups of interest.
clean	logical. Only return factor columns not defined in metadataBlacklist.
return	Object class to return. Uses match.arg() internally and picks the first item in the vector by default.
value	Value to assign.

Value

Data describing the samples.

Author(s)

Michael Steinbaugh

See Also

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

Examples

# SingleCellExperiment ====
x <- cellranger_small
sampleData(x, clean = FALSE) %>% glimpse()
sampleData(x, clean = TRUE) %>% glimpse()

# Assignment support
sampleData(x)[["batch"]] <- 1L
sampleData(x) %>% glimpse()

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