BASiCS_Filter {BASiCS} | R Documentation |
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.
BASiCS_Filter( Counts, Tech = rep(FALSE, nrow(Counts)), SpikeInput = NULL, BatchInfo = NULL, MinTotalCountsPerCell = 2, MinTotalCountsPerGene = 2, MinCellsWithExpression = 2, MinAvCountsPerCellsWithExpression = 2 )
Counts |
Matrix of dimensions |
Tech |
Logical vector of length |
SpikeInput |
Vector of length |
BatchInfo |
Vector of length |
MinTotalCountsPerCell |
Minimum value of total expression counts
required per cell (biological and technical).
Default: |
MinTotalCountsPerGene |
Minimum value of total expression counts
required per transcript (biological and technical).
Default: |
MinCellsWithExpression |
Minimum number of cells where expression
must be detected (positive count). Criteria applied to each transcript.
Default: |
MinAvCountsPerCellsWithExpression |
Minimum average number of
counts per cells where expression is detected. Criteria applied to
each transcript. Default 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
Catalina A. Vallejos cnvallej@uc.cl
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),]