################################################################################
################ extdata/expected_normalizedMatrix.Rdat ######################
################################################################################
##
## This object is a SingleCellExperiment object created by CONCLUS after the
## normalisation.
##
## This is the code to generate this object:
library(conclus)
## Loading of the count matrix
countMatrixPath <- file.path(system.file("extdata", package = "conclus"),
"countMatrix.tsv")
countMatrix <- loadDataOrMatrix(file=countMatrixPath, type="countMatrix",
ignoreCellNumber=TRUE)
## Loading of the count matrix
columnsMetaDataPath <- file.path(system.file("extdata", package = "conclus"),
"colData.tsv")
columnsMetaData <- loadDataOrMatrix(file=columnsMetaDataPath, type="coldata",
columnID="cell_ID")
## Creation of the singlecellRNAseq object
scrLight <- singlecellRNAseq(experimentName = "LightExperience",
countMatrix = countMatrix,
species = "mouse",
outputDirectory = "YourOutputDirectory")
## Normalization
scrNorm <- normaliseCountMatrix(scrLight, coldata=columnsMetaData, info=FALSE)
## Retrieved the SingleCellExperiment object
expectedNormalizedMatrix <- getSceNorm(scrNorm)
## Save the object
file <- "inst/extdata/expected_normalizedMatrix.Rdat"
save(expectedNormalizedMatrix, file=file)
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