R: Creates a SingleCellExperiment object from a matrix of...

newBASiCS_Data {BASiCS}

R Documentation

Creates a SingleCellExperiment object from a matrix of expression counts and experimental information about spike-in genes

Description

newBASiCS_Data creates a SingleCellExperiment object from a matrix of expression counts and experimental information about spike-in genes.

Usage

newBASiCS_Data(
  Counts,
  Tech = rep(FALSE, nrow(Counts)),
  SpikeInfo = NULL,
  BatchInfo = NULL,
  SpikeType = "ERCC"
)

Arguments

`Counts`	Matrix of dimensions `q` times `n` whose elements contain the expression counts to be analyses (including biological and technical spike-in genes). Gene names must be stored as `rownames(Counts)`.
`Tech`	Logical vector of length `q`. If `Tech = FALSE` the gene is biological; otherwise the gene is spike-in. Defaul value: `Tech = rep(FALSE, nrow(Counts))`.
`SpikeInfo`	`data.frame` whose first and second columns contain the gene names assigned to the spike-in genes (they must match the ones in `rownames(Counts)`) and the associated input number of molecules, respectively. If `SpikeInfo = NULL`, only the horizontal integration implementation (no spikes) can be run. Default value: `SpikeInfo = NULL`.
`BatchInfo`	Vector of length `n` whose elements indicate batch information. Not required if a single batch is present on the data. Default value: `BatchInfo = NULL`.
`SpikeType`	Character to indicate what type of spike-ins are in use. Default value: `SpikeType = "ERCC"` (parameter is no longer used).

Value

An object of class SingleCellExperiment.

Author(s)

Catalina A. Vallejos cnvallej@uc.cl

Nils Eling eling@ebi.ac.uk

Examples


## Data with spike-ins

# Expression counts
set.seed(1)
Counts <- matrix(rpois(50*10, 2), ncol = 10)
rownames(Counts) <- c(paste0('Gene', 1:40), paste0('ERCC', 1:10))
# Technical information
Tech <- grepl("ERCC", rownames(Counts))
# Spikes input number of molecules
set.seed(2)
SpikeInfo <- data.frame(gene = rownames(Counts)[Tech],
                        amount = rgamma(10, 1, 1))

# Creating a BASiCS_Data object (no batch effect)
DataExample <- newBASiCS_Data(Counts, Tech = Tech, SpikeInfo = SpikeInfo)

# Creating a BASiCS_Data object (with batch effect)
BatchInfo <- c(rep(1, 5), rep(2, 5))
DataExample <- newBASiCS_Data(Counts, Tech = Tech,
                              SpikeInfo = SpikeInfo, BatchInfo = BatchInfo)

## Data without spike-ins (BatchInfo is required)

# Expression counts
set.seed(1)
Counts <- matrix(rpois(50*10, 2), ncol = 10)
rownames(Counts) <- paste0('Gene', 1:50)
BatchInfo <- c(rep(1, 5), rep(2, 5))

# Creating a BASiCS_Data object (with batch effect)
DataExample <- newBASiCS_Data(Counts, BatchInfo = BatchInfo)

[Package BASiCS version 1.8.1 Index]