BASiCS (version 0.7.30)

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

Description

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

Usage

newBASiCS_Data(Counts, Tech, SpikeInfo, BatchInfo = NULL)

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.

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.

BatchInfo

Vector of length n whose elements indicate batch information.

Value

An object of class BASiCS_Data-class.

References

Vallejos, Marioni and Richardson (2015). Bayesian Analysis of Single-Cell Sequencing data.

See Also

BASiCS_Data-class

Examples

# NOT RUN {

# Expression counts
set.seed(1)
Counts = Counts = matrix(rpois(50*10, 2), ncol = 10)
rownames(Counts) <- c(paste0("Gene", 1:40), paste0("Spike", 1:10))

# Technical information
Tech = c(rep(FALSE,40),rep(TRUE,10))

# 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, SpikeInfo)

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

# Thanks to Simon Andrews for reporting an issue in previous version of this documentation

# }