MAST
Model-based Analysis of Single Cell Transcriptomics

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56
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MAST: Model-based Analysis of Single Cell Transcriptomics
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API

API for MAST
Model-based Analysis of Single Cell Transcriptomics

Global functions
"ZlmFit-summary" Man page
"summary-ZlmFit", Man page
.approxt Source code
.bayesglm.fit.loop.validateInputs Source code
.dexpit Source code
.dispersion Source code
.expit Source code
.fit Source code
.glmDOF Source code
.internalfilter Source code
.lrTest Source code
.lrtZlmFit Source code
.makeContrastMatrixFromCoefficientHypothesis Source code
.residualsD Source code
.rotateMM Source code
.waldTest Source code
.zlm Source code
BayesGLMlike-class Man page
CoefficientHypothesis Man page Source code
CovFromBoots Man page Source code
Drop Man page Source code
FluidigmAssay Man page
FromFlatDF Man page Source code
FromMatrix Man page Source code
GLMlike-class Man page
GSEATests-class Man page
Glue Source code
Hypothesis Man page
LMERlike-class Man page
LMlike-class Man page
LRT Man page
LRT,SingleCellAssay,character-method Man page
MAST Man page
MAST-defunct Man page
MAST-package Man page
SceToSingleCellAssay Man page Source code
SingleCellAssay Man page
ZlmFit Man page
ZlmFit-class Man page
applyFlat Man page Source code
apply_by Source code
assay,SingleCellAssay,missing-method Man page
assay_idx Man page Source code
bayesglm.influence Source code
bootVcov1 Man page Source code
burdenOfFiltering Man page Source code
cData Man page
calcZ Man page Source code
callName Source code
check.vars Source code
checkAssayNames Source code
checkGroups Source code
coef,LMERlike-method Man page
coef,ZlmFit-method Man page
colData<-,SingleCellAssay,DataFrame-method Man page
collectResiduals Man page Source code
collectSummaries Source code
combined_residuals_hook Man page Source code
complexifyNA Source code
computeEtFromCt Man page Source code
condSd Man page Source code
condmean Man page Source code
continuous_residuals_hook Man page Source code
convertMASTClassicToSingleCellAssay Man page Source code
defaultAssay Man page
defaultPrior Man page Source code
deviance_residuals_hook Man page
diag_safeContrastQF Source code
discrete_residuals_hook Man page Source code
dof Man page
dof,GLMlike-method Man page
dof,LMERlike-method Man page
ebayes Man page Source code
ell Source code
escapeSymbols Source code
expavg Man page Source code
exprs Man page
fData Man page
filter Man page
filterLowExpressedGenes Man page Source code
fit Man page
fit,BayesGLMlike,missing-method Man page
fit,GLMlike,missing-method Man page
fit,LMERlike,missing-method Man page
fitted_phat Man page Source code
fixdf Source code
freq Man page Source code
generateHypothesis Source code
genewiseMult Source code
getConcordance Man page Source code
getLogFC Man page Source code
getMarginalHyperLikelihood Source code
getQr Source code
getREvars Source code
getSSg_rNg Source code
getrc Man page Source code
getss Man page Source code
getwellKey Man page
getwellKey,SingleCellAssay-method Man page
getwss Man page Source code
gseaAfterBoot Man page Source code
gsea_control Man page Source code
hushWarning Man page Source code
impute Man page Source code
influence.bayesglm Man page
invlogit Man page
listType Source code
logFC Man page Source code
logLik,GLMlike-method Man page
logLik,LMERlike-method Man page
logProd Source code
logmean Man page Source code
logshift Source code
lrTest Man page
lrTest,LMlike,CoefficientHypothesis-method Man page
lrTest,LMlike,Hypothesis-method Man page
lrTest,LMlike,character-method Man page
lrTest,LMlike,matrix-method Man page
lrTest,ZlmFit,CoefficientHypothesis-method Man page
lrTest,ZlmFit,Hypothesis-method Man page
lrTest,ZlmFit,character-method Man page
lrTest,ZlmFit,matrix-method Man page
lrt Source code
lrtest Source code
magic_assay_names Man page Source code
maits Man page
makeChiSqTable Source code
mast_filter Man page Source code
melt.SingleCellAssay Man page Source code
mkunique Source code
model.matrix Man page
model.matrix,LMlike-method Man page
model.matrix<- Man page
model.matrixBayes Source code
myBiplot Man page Source code
normalci Source code
numexp Man page Source code
orderCutpoints Source code
partialScore Man page Source code
pbootVcov1 Man page
plot.thresholdSCRNACountMatrix Man page Source code
plotSCAConcordance Man page Source code
plotlrt Man page Source code
predict.ZlmFit Man page Source code
predicted_sig Man page
primerAverage Man page Source code
print.summaryThresholdSCRNA Man page Source code
print.summaryZlmFit Man page Source code
read.fluidigm Man page Source code
read.fluidigm.xls Source code
removeResponse Man page Source code
reraise Source code
residualsHook Source code
revealHook Source code
rowm Source code
rstandard.bayesglm Man page
safeCP Source code
safeContrastDP Source code
safeContrastQF Source code
sanity_check_sca Source code
sca_assay Source code
sca_assay_replace Source code
se.coef Man page
se.coef,ZlmFit-method Man page
show,LMlike-method Man page
show,ZlmFit-method Man page
solveMoM Source code
split,SingleCellAssay,character-method Man page
split,SingleCellAssay,factor-method Man page
split,SingleCellAssay,list-method Man page
stat_ell Man page Source code
subset,SingleCellAssay-method Man page
summarize Man page
summary,GSEATests-method Man page
summary,LMlike-method Man page
summary,ZlmFit-method Man page
summary.thresholdSCRNACountMatrix Man page Source code
summary.zlm Source code
thresholdSCRNACountMatrix Man page Source code
toAdditiveFormula Source code
toAdditiveString Source code
torowm Source code
uncomplexify Source code
uniqueModNA Source code
uniqueModNA.old Source code
update,LMERlike-method Man page
update,LMlike-method Man page
vbeta Man page
vbetaFA Man page
vcov,GLMlike-method Man page
vcov,LMERlike-method Man page
vcov,ZlmFit-method Man page
waldTest Man page
waldTest,LMlike,CoefficientHypothesis-method Man page
waldTest,LMlike,matrix-method Man page
waldTest,ZlmFit,CoefficientHypothesis-method Man page
waldTest,ZlmFit,Hypothesis-method Man page
waldTest,ZlmFit,matrix-method Man page
xform Man page Source code
zlm Man page Source code
zlm.SingleCellAssay Man page
MAST documentation built on Nov. 8, 2020, 8:19 p.m.

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