BASiCS_Filter: Filter for input datasets

In catavallejos/BASiCS: Bayesian Analysis of Single-Cell Sequencing data

Filter for input datasets

Description

BASiCS_Filter indicates which transcripts and cells pass a pre-defined inclusion criteria. The output of this function used to generate a SingleCellExperiment object required to run BASiCS. For more systematic tools for quality control, please refer to the scater Bioconductor package.

Usage

BASiCS_Filter(
  Counts,
  Tech = rep(FALSE, nrow(Counts)),
  SpikeInput = NULL,
  BatchInfo = NULL,
  MinTotalCountsPerCell = 2,
  MinTotalCountsPerGene = 2,
  MinCellsWithExpression = 2,
  MinAvCountsPerCellsWithExpression = 2
)

Arguments

Counts	Matrix of dimensions q times n whose elements corresponds to the simulated expression counts. First q.bio rows correspond to biological genes. Last q-q.bio rows correspond to technical spike-in genes.
Tech	Logical vector of length q. If Tech = FALSE the gene is biological; otherwise the gene is spike-in.
SpikeInput	Vector of length q-q.bio whose elements indicate the simulated input concentrations for the spike-in genes.
BatchInfo	Vector of length n whose elements indicate batch information. Not required if a single batch is present on the data. Default: BatchInfo = NULL.
MinTotalCountsPerCell	Minimum value of total expression counts required per cell (biological and technical). Default: MinTotalCountsPerCell = 2.
MinTotalCountsPerGene	Minimum value of total expression counts required per transcript (biological and technical). Default: MinTotalCountsPerGene = 2.
MinCellsWithExpression	Minimum number of cells where expression must be detected (positive count). Criteria applied to each transcript. Default: MinCellsWithExpression = 2.
MinAvCountsPerCellsWithExpression	Minimum average number of counts per cells where expression is detected. Criteria applied to each transcript. Default value: MinAvCountsPerCellsWithExpression = 2.

Value

A list of 2 elements

Counts

Filtered matrix of expression counts

Tech

Filtered vector of spike-in indicators

SpikeInput

Filtered vector of spike-in genes input molecules

BatchInfo

Filtered vector of the 'BatchInfo' argument

IncludeGenes

Inclusion indicators for transcripts

IncludeCells

Inclusion indicators for cells

Author(s)

Catalina A. Vallejos [e-mail]

Examples

set.seed(1)
Counts <- matrix(rpois(50*10, 2), ncol = 10)
rownames(Counts) <- c(paste0('Gene', 1:40), paste0('Spike', 1:10))
Tech <- c(rep(FALSE,40),rep(TRUE,10))
set.seed(2)
SpikeInput <- rgamma(10,1,1)
SpikeInfo <- data.frame('SpikeID' = paste0('Spike', 1:10),
                        'SpikeInput' = SpikeInput)

Filter <- BASiCS_Filter(Counts, Tech, SpikeInput,
                        MinTotalCountsPerCell = 2,
                        MinTotalCountsPerGene = 2,
                        MinCellsWithExpression = 2,
                        MinAvCountsPerCellsWithExpression = 2)
SpikeInfoFilter <- SpikeInfo[SpikeInfo$SpikeID %in% rownames(Filter$Counts),]

catavallejos/BASiCS documentation built on March 27, 2024, 12:49 a.m.