A B C D E F G H I L M N P R S T U V W X Z
MAST-package | MAST: Model-based Analysis of Single- cell Transcriptomics |
applyFlat | Apply a vectorized binary operation recycling over last dimension |
BayesGLMlike-class | Wrapper for bayesian GLM |
bootVcov1 | Bootstrap a zlmfit |
burdenOfFiltering | Filter a SingleCellAssay |
calcZ | Get Z or T statistics and P values after running gseaAfterBoot |
cData | Deprecated cell/feature data accessors/mutators |
cData-method | Deprecated cell/feature data accessors/mutators |
cData<- | Deprecated cell/feature data accessors/mutators |
cData<--method | Deprecated cell/feature data accessors/mutators |
coef-method | Wrapper for lmer/glmer |
coef-method | An S4 class to hold the output of a call to zlm |
CoefficientHypothesis | Describe a linear model hypothesis to be tested |
colData<--method | Replace 'colData' |
collectResiduals | Residual hooks and collection methods |
combine-method | Deprecated cell/feature data accessors/mutators |
combined_residuals_hook | Residual hooks and collection methods |
computeEtFromCt | Compute the Et from the Ct |
condmean | Report the mean et value for each gene |
condSd | Report standard deviation of et, for positive et for each gene |
continuous_residuals_hook | Residual hooks and collection methods |
convertMASTClassicToSingleCellAssay | Convert a MASTClassic SingleCellAssay |
defaultPrior | Initialize a prior to be used a prior for BayeGLMlike/BayesGLMlike2 |
deviance_residuals_hook | Residual hooks and collection methods |
discrete_residuals_hook | Residual hooks and collection methods |
dof | Degrees of freedom of Zero inflated model |
dof-method | Degrees of freedom of Zero inflated model |
Drop | Drop specified dimension from an array |
ebayes | Estimate hyperparameters for hierarchical variance model for continuous component |
expavg | Exponential average |
fData | fData |
fData-method | fData |
featureData | Accessor for featureData 'AnnotatedDataFrame' |
featureData-method | Accessor for featureData 'AnnotatedDataFrame' |
filter | Filter a SingleCellAssay |
filterLowExpressedGenes | Filter low-expressing genes |
fit | fit a zero-inflated regression |
fit-method | fit a zero-inflated regression |
fitted_phat | Residual hooks and collection methods |
FluidigmAssay | Construct a SingleCellAssay (or derived subclass) from a 'flat' (melted) data.frame/data.table |
freq | Report the proportion of expression for each gene |
FromFlatDF | Construct a SingleCellAssay (or derived subclass) from a 'flat' (melted) data.frame/data.table |
FromMatrix | Construct a SingleCellAssay from a matrix or array of expression |
getConcordance | getConcordance |
getLogFC | Calculate log-fold changes from hurdle model components |
getrc | getConcordance |
getss | getConcordance |
getwellKey | Accessor for wellKey |
getwellKey-method | Accessor for wellKey |
getwss | getConcordance |
GLMlike-class | Wrapper for regular glm/lm |
gseaAfterBoot | Gene set analysis for hurdle model |
GSEATests-class | An S4 class for Gene Set Enrichment output |
hushWarning | Selectively muffle warnings based on output |
Hypothesis | Describe a linear model hypothesis to be tested |
impute | impute missing continuous expression for plotting |
influence.bayesglm | Influence bayesglm object |
invlogit | Inverse of logistic transformation |
LMERlike-class | Wrapper for lmer/glmer |
LMlike-class | Linear Model-like Class |
logFC | Calculate log-fold changes from hurdle model components |
logLik-method | Wrapper for lmer/glmer |
logLik-method | Linear Model-like Class |
logmean | Log mean |
LRT | Likelihood Ratio Tests for SingleCellAssays |
LRT-method | Likelihood Ratio Tests for SingleCellAssays |
lrTest | Run a likelihood-ratio test |
lrTest-method | Linear Model-like Class |
lrTest-method | An S4 class to hold the output of a call to zlm |
lrTest-method | Likelihood ratio test |
maits | MAITs data set, RNASeq |
MAST | MAST: Model-based Analysis of Single- cell Transcriptomics |
melt.SingleCellAssay | Melt a rectangular array |
model.matrix | Model matrix accessor |
model.matrix-method | Model matrix accessor |
model.matrix<- | Replace model matrix |
myBiplot | Makes a nice BiPlot |
numexp | Report number of expressing cells per gene |
partialScore | Residual hooks and collection methods |
pbootVcov1 | Bootstrap a zlmfit |
plot.thresholdSCRNACountMatrix | Plot cutpoints and densities for thresholding |
plotlrt | Plot a likelihood ratio test object |
plotSCAConcordance | Concordance plots of filtered single vs n-cell assays |
predict.ZlmFit | Return predictions from a ZlmFit object. |
primerAverage | Average within duplicated genes/primers |
print.summaryThresholdSCRNA | Summarize the effect of thresholding |
print.summaryZlmFit | Print summary of a ZlmFit |
read.fluidigm | read.fluidigm |
removeResponse | Remove the left hand side (response) from a formula |
rstandard.bayesglm | rstandard for bayesglm objects. |
se.coef | Return coefficient standard errors |
se.coef-method | An S4 class to hold the output of a call to zlm |
show-method | show |
SingleCellAssay | Construct a SingleCellAssay (or derived subclass) from a 'flat' (melted) data.frame/data.table |
split-method | Split into 'list' |
stat_ell | Plot confidence ellipse in 2D |
subset-method | Subset a 'SingleCellAssay' by cells (columns) |
summarize | Return programmatically useful summary of a fit |
summary-method | Linear Model-like Class |
summary-method | Summarize gene set enrichment tests |
summary-method | Summarize model features from a 'ZlmFit' object |
summary.thresholdSCRNACountMatrix | Summarize the effect of thresholding |
thresholdSCRNACountMatrix | Threshold a count matrix using an adaptive threshold. |
update-method | Wrapper for lmer/glmer |
update-method | Linear Model-like Class |
vbeta | Vbeta Data Set |
vbetaFA | Vbeta Data Set, FluidigmAssay |
vcov-method | Wrapper for regular glm/lm |
vcov-method | Wrapper for lmer/glmer |
vcov-method | An S4 class to hold the output of a call to zlm |
waldTest | Run a Wald test |
waldTest-method | Linear Model-like Class |
waldTest-method | An S4 class to hold the output of a call to zlm |
waldTest-method | Wald test |
xform | Make matrix of continuous expression values, orthogonal to discrete |
zlm | Convenience function for running a zero-inflated regression |
zlm.SingleCellAssay | Zero-inflated regression for SingleCellAssay |
ZlmFit-class | An S4 class to hold the output of a call to zlm |