BASiCS_TestDE {BASiCS} | R Documentation |
Function to assess changes in expression between two groups of cells (mean and over-dispersion)
BASiCS_TestDE(Chain1, Chain2, EpsilonM = log2(1.5), EpsilonD = log2(1.5), EpsilonR = log2(1.5)/log2(exp(1)), ProbThresholdM = NULL, ProbThresholdD = NULL, ProbThresholdR = NULL, OrderVariable = "GeneIndex", GroupLabel1 = "Group1", GroupLabel2 = "Group2", Plot = TRUE, PlotOffset = TRUE, Offset = TRUE, EFDR_M = 0.1, EFDR_D = 0.1, EFDR_R = 0.1, GenesSelect = NULL, ...)
Chain1 |
an object of class |
Chain2 |
an object of class |
EpsilonM |
Minimum fold change tolerance threshold for detecting
changes in overall expression (must be a positive real number).
Default value: |
EpsilonD |
Minimum fold change tolerance threshold for detecting
changes in biological over-dispersion (must be a positive real number).
Default value: |
EpsilonR |
Minimum distance threshold for detecting
changes in residual over-dispersion (must be a positive real number).
Default value: |
ProbThresholdM |
Optional parameter. Probability threshold for detecting changes in overall expression (must be a positive value, between 0 and 1) |
ProbThresholdD |
Optional parameter. Probability threshold for detecting changes in cell-to-cell biological over-dispersion (must be a positive value, between 0 and 1) |
ProbThresholdR |
Optional parameter. Probability threshold for detecting changes in residual over-dispersion (must be a positive value, between 0 and 1) |
OrderVariable |
Ordering variable for output.
Possible values: |
GroupLabel1 |
Label assigned to reference group.
Default: |
GroupLabel2 |
Label assigned to reference group.
Default: |
Plot |
If |
PlotOffset |
If |
Offset |
Optional argument to remove a fix offset effect (if not
previously removed from the MCMC chains). Default: |
EFDR_M |
Target for expected false discovery rate related to
the comparison of means. Default |
EFDR_D |
Target for expected false discovery rate related to
the comparison of dispersions. Default |
EFDR_R |
Target for expected false discovery rate related to
the comparison of residual over-dispersions. Default |
GenesSelect |
Optional argument to provide a user-defined list
of genes to be considered for the comparison.
Default: |
... |
Graphical parameters (see |
BASiCS_TestDE
returns a list of 4 elements:
TableMean
A data.frame
containing the
results of the differential mean test
GeneName
Gene name
MeanOverall
For each gene, the estimated mean expression parameter μ_i is averaged across both groups of cells (weighted by sample size).
Mean1
Estimated mean expression parameter μ_i for each biological gene in the first group of cells.
Mean2
Estimated mean expression parameter μ_i for each biological gene in the second group of cells.
MeanFC
Fold change in mean expression parameters between the first and second groups of cells.
MeanLog2FC
Log2-transformed fold change in mean expression between the first and second groups of cells.
ProbDiffMean
Posterior probability for mean expression difference between the first and second groups of cells.
ResultDiffExp
Indicator if a gene has a higher mean expression in the first or second groups of cells.
TableDisp
A data.frame
containing the
results of the differential dispersion test (excludes genes for which
the mean does not changes).
GeneName
Gene name
MeanOverall
For each gene, the estimated mean expression parameter μ_i is averaged across both groups of cells (weighted by sample size).
DispOverall
For each gene, the estimated over-dispersion parameter δ_i is averaged across both groups of cells (weighted by sample size).
Disp1
Estimated over-dispersion parameter δ_i for each biological gene in the first group of cells.
Disp2
Estimated over-dispersion parameter δ_i for each biological gene in the second group of cells.
DispFC
Fold change in over-dispersion parameters between the between the first and second groups of cells.
DispLog2FC
Log-transformed fold change in over-dispersion between the first and second groups of cells.
ProbDiffDisp
Posterior probability for over-dispersion difference between the first and second groups of cells.
ResultDiffDisp
Indicator if a gene has a higher over-dispersion in the first or second groups of cells. Genes labelled with "ExcludedFromTest" were detected as showing differential mean expression.
TableResDisp
A data.frame
containing the
results of the differential residual over-dispersion test.
GeneName
Gene name
MeanOverall
For each gene, the estimated mean expression parameter μ_i is averaged across both groups of cells (weighted by sample size).
ResDispOverall
For each gene, the estimated residual over-dispersion parameter δ_i is averaged across both groups of cells (weighted by sample size).
ResDisp1
Estimated residual over-dispersion parameter ε_i for each biological gene in the first group of cells.
ResDisp2
Estimated residual over-dispersion parameter ε_i for each biological gene in the second group of cells.
ResDispDistance
Difference in residual over-dispersion between the first and second groups of cells.
ProbDiffResDisp
Posterior probability for residual over-dispersion difference between the first and second groups of cells.
ResultDiffResDisp
Indicator if a gene has a higher residual over-dispersion in the first or second groups of cells. Genes labelled with "ExcludedFromTest" were not expressed in at least 2 cells per condition.
DiffMeanSummary
A list containing the following information for the differential mean expression test:
ProbThreshold
Posterior probability threshold.
EFDR
Expected false discovery rate for the given thresholds.
EFNR
Expected false negative rate for the given thresholds.
DiffDispSummary
A list containing the following information for the differential over-dispersion test:
ProbThreshold
Posterior probability threshold.
EFDR
Expected false discovery rate for the given thresholds.
EFNR
Expected false negative rate for the given thresholds.
DiffResDispSummary
A list containing the following information for the differential residual over-dispersion test:
ProbThreshold
Posterior probability threshold.
EFDR
Expected false discovery rate for the given thresholds.
EFNR
Expected false negative rate for the given thresholds.
Chain1_offset
an BASiCS_Chain
object:
Chain1
after offset removal.
Chain2_offset
an BASiCS_Chain
object:
Chain2
after offset removal (this is only provided for
completeness; Chain2
is not affected by the offset).
OffsetChain
MCMC chain calculated for the offset effect.
Offset
Estimated offset (posterior median of
OffsetChain
). Default value set equal to 1 when offset
correction is not performed.
Catalina A. Vallejos cnvallej@uc.cl
Nils Eling eling@ebi.ac.uk
# Loading two 'BASiCS_Chain' objects (obtained using 'BASiCS_MCMC') data(ChainSC) data(ChainRNA) Test <- BASiCS_TestDE(Chain1 = ChainSC, Chain2 = ChainRNA, GroupLabel1 = 'SC', GroupLabel2 = 'P&S', EpsilonM = log2(1.5), EpsilonD = log2(1.5), OffSet = TRUE) # Results for the differential mean test head(Test$TableMean) # Results for the differential over-dispersion test # This only includes genes marked as 'NoDiff' in Test$TableMean head(Test$TableDisp) # For testing differences in residual over-dispersion, two chains obtained # via 'BASiCS_MCMC(Data, N, Thin, Burn, Regression=TRUE)' need to be provided data(ChainSCReg) data(ChainRNAReg) Test <- BASiCS_TestDE(Chain1 = ChainSCReg, Chain2 = ChainRNAReg, GroupLabel1 = 'SC', GroupLabel2 = 'P&S', EpsilonM = log2(1.5), EpsilonD = log2(1.5), EpsilonR = log2(1.5)/log2(exp(1)), OffSet = TRUE)