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. For more details see argument 'type' in see 'help(isSpike, package = "SingleCellExperiment")'. Default value: SpikeType = "ERCC".

Value

An object of class SingleCellExperiment.

Author(s)

Catalina A. Vallejos cnvallej@uc.cl

Nils Eling eling@ebi.ac.uk

See Also

SingleCellExperiment

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 1.6.0 Index]