calculateEvalMetrics | R Documentation |
Calculate evaluation metrics for bulk RNA-seq samples from test data to
understand model performance. By default, absolute error (AbsErr
),
proportional absolute error (ppAbsErr
), squared error (SqrErr
)
and proportional squared error (ppSqrErr
) are calculated for each test
sample. In addition, each of these metrics is aggregated using their mean
values according to three criteria: each cell type (CellType
),
probability bins in ranges of 0.1 (pBin
) and number of different cell
types present in the sample nCellTypes
. Finally, the process is
repeated only considering bulk samples (filtering out single-cell profiles
from the evaluation). The evaluation metrics will be available in the
test.deconv.metrics
slot of the
DigitalDLSorterDNN
object (trained.model
slot of
the DigitalDLSorter
object).
calculateEvalMetrics(object, metrics = c("MAE", "MSE"))
object |
|
metrics |
Metrics used to evaluate the model performance. Mean absolute
error ( |
A DigitalDLSorter
object with the
trained.model
slot containing a
DigitalDLSorterDNN
object with the
test.deconv.metrics
slot. The last contains the metrics calculated.
distErrorPlot
corrExpPredPlot
blandAltmanLehPlot
barErrorPlot
## Not run: set.seed(123) sce <- SingleCellExperiment::SingleCellExperiment( assays = list( counts = matrix( rpois(30, lambda = 5), nrow = 15, ncol = 20, dimnames = list(paste0("Gene", seq(15)), paste0("RHC", seq(20))) ) ), colData = data.frame( Cell_ID = paste0("RHC", seq(20)), Cell_Type = sample(x = paste0("CellType", seq(6)), size = 20, replace = TRUE) ), rowData = data.frame( Gene_ID = paste0("Gene", seq(15)) ) ) DDLS <- loadSCProfiles( single.cell.data = sce, cell.ID.column = "Cell_ID", gene.ID.column = "Gene_ID" ) probMatrixValid <- data.frame( Cell_Type = paste0("CellType", seq(6)), from = c(1, 1, 1, 15, 15, 30), to = c(15, 15, 30, 50, 50, 70) ) DDLS <- generateBulkCellMatrix( object = DDLS, cell.ID.column = "Cell_ID", cell.type.column = "Cell_Type", prob.design = probMatrixValid, num.bulk.samples = 50, verbose = TRUE ) # training of DDLS model tensorflow::tf$compat$v1$disable_eager_execution() DDLS <- trainDigitalDLSorterModel( object = DDLS, on.the.fly = TRUE, batch.size = 15, num.epochs = 5 ) # evaluation using test data DDLS <- calculateEvalMetrics( object = DDLS ) ## End(Not run)
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