API for statOmics/MSqRob
Robust statistical inference for quantitative LC-MS proteomics

Global functions
.ProtLM.print Source code
.Protdata.print Source code
.checkPredictors Source code
.createLmList Source code
.createParsedFormula Source code
.createRidgeList Source code
.emptyLM Source code
.emptylmerMod Source code
.errorCheckFit Source code
.getBetaVcovDfLm Source code
.getBetaVcovDfMermod Source code
.getDfLm Source code
.getDfMermod Source code
.getMoreLevels Source code
.getSigmaLm Source code
.getSigmaMermod Source code
.lmEstM3 Source code
.makeFormulaPredictors Source code
.normaliseMSnSet Source code
.normalizeRLR Source code
.protLM.valid Source code
.protdata.valid Source code
.removeSingleLevels Source code
.replaceFixed Source code
.ridgeEstM3 Source code
.squeezeVarRob Source code
.weightsLmFit Source code
MSnSet2protdata Man page Source code
[,protLM,ANY,ANY,ANY-method Man page
[,protdata,ANY,ANY,ANY-method Man page
addColClasses Source code
addFactorInteractions Man page Source code
addVarFromVar Man page Source code
addZerosQR Source code
adjustNames Man page Source code
adjust_stage2 Source code
aggregateMSnSet Source code
calculate_qvals Source code
check_expAnn Source code
contr.ltfr_MSqRob Man page Man page
countPeptides Man page Source code
cutOffPval Man page Source code
devFun Source code
devianceForHessian Source code
df2protdata Man page Source code
dfBetweenWithin Source code
dfSatterthwaite Source code
dummyVars_MSqRob Man page
dummyVars_MSqRob.default Man page Man page
fdrtool_subset Man page
fit.model Man page Source code
fitFDistRobustly_LG Source code
fitFDist_LG Source code
getAccessions,protLM-method Man page
getAccessions,protdata-method Man page
getAnnotationRun Source code
getAnnotations,protLM-method Man page
getAnnotations,protdata-method Man page
getBetaVcovDf,glm-method Man page
getBetaVcovDf,glmerMod-method Man page
getBetaVcovDf,lm-method Man page
getBetaVcovDf,lmerMod-method Man page
getBetaVcovDfList Man page Source code
getComp_preds Source code
getData,protdata-method Man page
getModels,protLM-method Man page
getN Source code
getPData,protdata-method Man page
getPartSet Source code
getPs Source code
getThetaVars Man page Source code
getVcovBetaBforGrad Source code
getXlevels Source code
get_qvals Man page Source code
import2MSnSet Man page Source code
importDIAData Man page
index2Numeric Man page Source code
init_ann_MQ_Excel Man page Source code
inspect_loads_MSqRob Man page
length,protLM-method Man page
length,protdata-method Man page
loads_MSqRob Man page
makeAnnotation Man page Source code
makeContrast Man page Source code
makeContrastMatrix Source code
make_pData_MSqRob Source code
pasteAnnotation Man page Source code
plot_fdrtool Man page Source code
predict.dummyVars_MSqRob Man page Man page Source code
preprocess_MSnSet Man page Source code
preprocess_MaxQuant Man page Source code
preprocess_generic Man page Source code
preprocess_long Man page Source code
preprocess_wide Man page Source code
print.protLM Source code
print.protdata Source code
prot.p.adjust Man page Source code
prot.p.adjust_protwise Man page Source code
prot.signif Man page Source code
protLM-class Man page
protdata-class Man page
read2MSnSet Man page Source code
read_MaxQuant Man page Source code
read_moFF Man page Source code
saves_MSqRob Man page
sechol Source code
selectAccessions,protdata-method Man page
setAccessions,protLM-method Man page
setAccessions,protdata-method Man page
setAnnotations,protLM-method Man page
setAnnotations,protdata-method Man page
setData,protdata-method Man page
setModels,protLM-method Man page
smallestUniqueGroups Man page Source code
squeezePars Man page Source code
squeezeThetas Man page Source code
squeezeVarRob Man page Source code
test.ANOVA Man page Source code
test.contrast Man page Source code
test.contrast_adjust Man page Source code
test.contrast_stagewise Man page Source code
test.protLMcontrast Man page Source code
update.lmerMod Man page Source code
updateProgress Source code
update_protLM Man page Source code
statOmics/MSqRob documentation built on May 20, 2020, 7:52 p.m.