API for xia-lab/MicrobiomeAnalystR
MicrobiomeAnalystR - A comprehensive R package for statistical, visual, and functional analysis of the microbiome.

Global functions
.checkSampleConsistencyMeta Source code
.compute.mummichogRTSigPvals Source code
.compute.mummichogSigPvals Source code
.do.anova Source code
.do.ttests Source code
.get.mbSetObj Source code
.getDynLoadPath Source code
.init.Permutations Source code
.init.RT.Permutations Source code
.load.scripts.on.demand Source code
.perform.computing Source code
.perform.mummichogRTPermutations Source code
.perform.my.maaslin Source code
.perform_edger Source code
.permanova_pairwise Source code
.prepare.batch Source code
.prepare.deseq Source code
.prepare.global Source code
.prepare.maaslin2 Source code
.prepare_rnaseq Source code
.read.microbiomeanalyst.lib.rds Man page Source code
.readDataTable Man page
.replace.by.lod Source code
.save.deseq.res Source code
.save.global.res Source code
.save.maaslin.res Source code
.search.compoundLib Source code
.set.mbSetObj Source code
.setup.library Source code
.to.numeric.mat Source code
AddErrMsg Man page Source code
AddFeatureToReport Source code
ApplyAbundanceFilter Man page Source code
ApplyAbundanceFilterMeta Man page Source code
ApplyMetaboFilter Man page Source code
ApplyVarianceFilter Man page Source code
ApplyVarianceFilterMeta Man page Source code
AutoNorm Source code
AutoScale Source code
CalculateHyperScore Man page Source code
CheckMetaDataIntegrity Man page Source code
CheckRawDataAlreadyNormalized Source code
CleanData Man page Source code
CleanTaxaNames Source code
ClearFactorStrings Source code
ClearRCommandHistory Source code
ClearStrings Source code
CompareMet Source code
CompareMic Source code
CompareSummaryStats Man page Source code
Compound_function_mzlist Source code
ComputeColorGradient Source code
ComputeColorGradientCorr Source code
ComputeEncasing Source code
ComputeGoods Source code
ComputeMummichogRTPermPvals Source code
Convert2Dictionary Source code
CoreMicrobeAnalysis Man page Source code
CreateFakeFile Source code
CreateFooter Man page
CreateMDPRnwReport Man page
CreateMMPFakeFile Source code
CreatePhyloseqObj Man page Source code
CreatePhyloseqObjMeta Man page Source code
CreateRHistAppendix Man page
CreateSDPRnwReport Man page
CreateStaticHeatmap Source code
CrossReferencing Man page Source code
D2K Source code
DeepCleanTaxaNames Source code
FeatureCorrelation Man page
GenerateTemplates Man page
GetAllDataNames Source code
GetBashFullPath Source code
GetBetaDiversityStats Source code
GetColorSchema Man page Source code
GetColorSchemaFromFactor Source code
GetCurrentImg Source code
GetCurrentMsg Source code
GetDataForPie Man page Source code
GetDatasetNamesString Source code
GetDiscreteInx Source code
GetErrMsg Man page Source code
GetExtendRange Source code Source code
GetFeatureNum Source code
GetFilesToBeSaved Source code
GetFinalNameMap Man page Source code
GetGeneListStat Man page Source code
GetGroupNamesMeta Source code
GetHTMLMetSet Source code
GetHighTaxaLvlNm Source code
GetHtGroupItems Source code
GetHtMetaCpInfo Source code
GetInitLib Source code
GetKeggProjectionType Source code
GetLibscale Source code
GetLowerTaxaLvlNm Source code
GetMapTable Man page
GetMetaByCol Source code
GetMetaCol Source code
GetMetaColLength Source code
GetMetaDataCol Source code
GetMetaDataGroups Source code Source code
GetMetaDataStatus Source code
GetMetaDatasets Source code
GetMetaGeneIDType Source code
GetMetaInfo Source code
GetMetaInfoMeta Source code
GetMetaResultColNames Source code
GetMetaResultGeneIDLinks Source code
GetMetaResultGeneIDs Source code
GetMetaResultGeneSymbols Source code
GetMetaResultMatrix Source code
GetMetaResultPathSymbols Source code
GetMetaSigGeneCount Source code
GetMetaStat Source code
GetMetaStatNames Source code
GetMetaSummary Source code
GetMetaTaxaInfo Source code
GetMetaTypes Source code
GetMetaboResColNames Source code
GetMetaboResRowNames Source code
GetMetadataMsg Source code
GetMsetEvidence Source code
GetMsetMembers Source code
GetMsetNames Source code
GetMsetPval Source code
GetMsetReferences Source code
GetNameMapCol Source code
GetNumOfLists Source code
GetNumbericalInx Source code
GetORA.colorBar Source code
GetORA.mat Source code
GetORA.rowNames Source code
GetORATable Man page Source code
GetOS Source code
GetOmicsDataDims Source code
GetOrigSmplGroupNamesPerMeta Source code
GetOrigSmplGroupNamesPerMetaInd Source code
GetOrigSmplNms Source code
GetOrigSmplNmsInd Source code
GetPieTaxaAbund Source code
GetPieTaxaNames Source code
GetRCommandHistory Source code
GetRFConf.Table Man page
GetRandomNumbers Source code
GetRawClassNms Source code
GetRawFileNms Source code
GetResColNames Source code
GetResColNamesMeta Source code
GetResMat Source code
GetResMatrix Source code
GetResMetabo Source code
GetResMetric Source code
GetResRowNames Source code Source code
GetSamplNames Source code
GetSampleGroups Source code
GetSampleGrpInfo Source code
GetSampleGrpNo Source code
GetSampleInfo Source code
GetSampleNamesaftNorm Source code
GetSampleNumber Source code
GetSanityVec Source code
GetSeriesColors Source code
GetShortNames Source code
GetSigGeneCount Source code
GetSigTable Source code
GetSigTable.Corr Man page
GetSigTable.LEFSE Man page
GetSigTable.METAGENOSEQ Man page
GetSigTable.RNASeq Man page
GetSigTable.UNIVAR Man page
GetStressNMDS Source code
GetSummaryData Source code
GetTaxaFeatSize Source code
GetTaxaNames Source code
GetTseaCol Source code
GetTseaRowNames Source code
GetUniqueMetaNames Source code
IncludeDataset Source code
Init.DataMeta Man page Source code
Init.mbSetObj Man page Source code
InitPieColors Source code
IsPoorReplicate Source code
IsTreeUploaded Source code
LoadKEGGKO_lib Source code
LogNorm Source code
MapKO2KEGGEdges Source code
Match.Pattern Man page
MergeDatasets Man page Source code
MessageOutput Source code
MiRKAT Source code
MiRKAT_continuous Source code
PCoA3D.Anal Man page Source code
PCoA3DAnal.16SRef Man page Source code
Perform16FunAnot Source code
Perform16FunAnot_mem Man page Source code
PerformAlphaDiversityComp Man page Source code
PerformAlphaGLM Source code
PerformBatchCorrection Man page Source code
PerformBetaDiversity Man page Source code
PerformCategoryComp Man page Source code
PerformDEAnalyse Man page Source code
PerformDataMerging Source code
PerformFastUnivTests Source code
PerformKOEnrichAnalysis_KO01100 Man page Source code
PerformKOEnrichAnalysis_List Source code
PerformKOProjection Man page Source code
PerformKOmapping Man page Source code
PerformLayOut Source code
PerformLefseAnal Man page Source code
PerformMantelTest Source code
PerformMetaEffectSize Man page Source code
PerformMetaboNormalization Man page Source code
PerformMetagenomeSeqAnal Man page Source code
PerformNetworkCorrelation Man page Source code
PerformNormalization Man page Source code
PerformNormalizationMeta Man page Source code
PerformPairDEAnalyse Source code
PerformPartialCorr Man page Source code
PerformRNAseqDE Man page Source code
PerformRarefaction Man page Source code
PerformRefDataMapping Man page Source code
PerformSeqCheck Source code
PerformSeqImport Source code
PerformSeqProcessing Source code
PerformUnivTests Source code
PerformUnivarTest Man page Source code
PlotAlphaBoxData Man page Source code
PlotAlphaData Man page Source code
PlotAlphaGLM Source code
PlotBetaSummary Man page
PlotBoxData Man page Source code
PlotBoxDataCorr Man page Source code
PlotBoxMultiData Source code
PlotBoxMultiMetabo Source code
PlotCorr Man page
PlotCovariateMap Source code
PlotCovariateMapMas Source code
PlotDataOverview Source code
PlotDataPieFromPie Man page Source code
PlotDataProfile Source code
PlotDensityView Source code
PlotEnrichNet.Overview Man page Source code
PlotFunAnotSummary Man page Source code
PlotFunctionStack Man page Source code
PlotGroupDataHeattree Source code
PlotGroupPieGraph Man page Source code
PlotHeatmap Man page Source code
PlotImpVar Man page Source code
PlotImpVarLEfSe Man page Source code
PlotLEfSeSummary Man page Source code
PlotLibSizeView Man page Source code
PlotMetaDensity Man page Source code
PlotMetaPCA Man page Source code
PlotOverallPieGraph Man page Source code
PlotOverviewDataHeattree Source code
PlotPCAView Man page Source code
PlotPhylogeneticTree Man page Source code
PlotPiechart Man page Source code
PlotRF.Classify Man page Source code
PlotRF.VIP Man page Source code
PlotRareCurve Man page Source code
PlotRarefactionCurve Man page Source code
PlotSampleDataHeattree Source code
PlotSamplePieGraph Man page Source code
PlotSampleTaxaAundanceBar Man page Source code
PlotSelectedFeature Source code
PlotSelectedSample Man page Source code
PlotTaxaAbundanceArea Man page Source code
PlotTaxaAbundanceBarSamGrp Man page Source code
PlotTaxaAundanceBar Man page Source code
PlotTreeGraph Man page Source code
PlotUsrRefPCoA3DScore Man page Source code
PlotlyCompManht Source code
PlotlyTaxaAbundance Source code
PostProcessMaaslin Source code
PrepareBoxPlot Source code
PrepareCorrExpValues Source code
PrepareDownloadData Source code
PrepareEnrichNet Man page Source code
PrepareHeatTreePlot Man page Source code
PrepareHeatTreePlotAbR Source code
PrepareHeatTreePlotDataParse_cmf Man page Source code
PrepareHeatTreePlotDataParse_cmf_diff_table Man page Source code
PrepareHeatTreePlotDataParse_cmf_plot Man page Source code
PrepareMergedData Man page Source code
PreparePCA4Shotgun Man page Source code
PreparePDFReport Man page
PrepareQueryJson Man page Source code
RF.Anal Man page Source code
Read16SAbundData Man page Source code
Read16SAbundDataMeta Man page Source code
Read16SBiomData Man page Source code
Read16STabData Man page Source code
Read16STaxaTable Man page Source code
Read16STaxaTableMeta Man page Source code
ReadDataForMetaInfo Source code
ReadMetabolicTable Man page Source code
ReadMothurData Man page Source code
ReadPeakList Source code
ReadRawMeta Source code
ReadSampleTable Man page Source code
ReadSampleTableMeta Man page Source code
ReadSampleTableMetaInd Man page Source code
ReadShotgunBiomData Man page Source code
ReadShotgunTabData Man page Source code
ReadTreeFile Man page Source code
RecordRCommand Source code
RemoveData Source code
RemoveDuplicates Source code
RemoveSelectedMeta Source code
RemoveSelectedMetaInd Source code
ReplaceMissingByLoD Source code
RunFastSpar Man page
SanityCheckData Man page Source code
SanityCheckDataMeta Man page Source code
SanityCheckMetData Man page Source code
SanityCheckSampleData Man page Source code
SanityCheckSampleDataMeta Man page Source code
Save2KEGGJSON Source code
SavePiechartImg Man page Source code
SelectData Source code
SelectRefData Source code
Set.Config Source code
SetCurrentData Source code Source code
SetCurrentMetaData Source code Source code
SetCurrentSelectedTaxLevel Source code
SetDataTypeOfMeta Man page Source code
SetGroupItems Source code
SetMetaAttributes Man page Source code
SetMetaTypes Source code
SetModuleType Man page Source code
SetParam Source code
SetSelMetaData Source code
SetTaxonSetLib Man page Source code
Setup.MapData Man page Source code
SetupMetaStats Source code
ShowMemoryUse Source code
SparccToNet Source code
SpeciesMappingExact Source code
SquareRootNorm Source code
Tax4Fun Source code
UnzipUploadedFile Source code
UpdateConfItems Man page Source code
UpdateListInput Man page Source code
UpdateMetaColName Source code
UpdateMetaColNameInd Source code
UpdateMetaData Source code
UpdateMetaLevels Source code
UpdateMetaLevelsInd Source code
UpdateMetaOrder Source code
UpdateMetaOrderInd Source code
UpdateMetaType Source code
UpdatePieData Man page Source code
UpdateSampleBasedOnLoading Source code
UpdateSampleGroups Source code
UpdateSampleGroupsInd Source code
UpdateSampleItems Man page Source code
UtilMakeCountTables Source code
UtilMakePhyloseqObjs Source code
ValidateFeatureName Source code
abn_est Source code
abundances Source code
assert_equal_class Source code
assert_equal_type Source code
assert_length_1_or_n Source code
blastTableReducer Source code
calcKRVstat Source code
calcRsquared Source code
calculate_Reads Source code
case_when Man page Source code
checkParing Source code
check_length_1_or_n Source code
checkfac Source code
cleanMem Source code
clr_transform Source code
color_scale Source code
composeParamFun Source code
condenseOTUs Man page Source code
core Source code
core_heatmap Source code
core_members Source code
create.adducts Source code
doKOFiltering Source code
edgeRnorm Source code
exportOTUtaxaInfo Source code
exportSampleNMs Source code
exportSampleTrackTable Source code
fast.write Source code
fast_tax_glom Source code
fast_tax_glom_first Source code
fast_tax_glom_mem Source code
filtKOmap Source code
generateColorArr Source code
generateColorGradient Source code
generatePCAscatter Source code
generateResFigures Source code
generate_breaks Source code
get.fun.lib.path Source code
getIdx Source code
getLambda_davies Source code
getQ Source code
getindivP_davies Source code
gg2list_new Source code
gg_color_hue Source code
gg_color_hue_scatter Source code
ggplotly_modified Source code
ggrare2 Source code
glm_qqplot Source code
gm_mean Source code
importTax4FunReferenceData Source code
inconsistent_lengths_message Source code
isEmptyMatrix Source code
libSizeQuickView Source code
load_MASS Source code
load_ape Source code
load_biocparallel Source code
load_biomformat Source code
load_cairo Source code
load_datatable Source code
load_deseq Source code
load_edgeR Source code
load_ggfortify Source code
load_ggplot Source code
load_ggraph Source code
load_ggrepel Source code
load_globaltest Source code
load_gplots Source code
load_grid Source code
load_gridExtra Source code
load_igraph Source code
load_iheatmapr Source code
load_metacoder Source code
load_metagenomeseq Source code
load_pheatmap Source code
load_phyloseq Source code
load_ppcor Source code
load_qs Source code
load_randomforest Source code
load_rcolorbrewer Source code
load_reshape Source code
load_splitstackshape Source code
load_stringr Source code
load_tax4fun Source code
load_vegan Source code
load_viridis Source code
load_visNetwork Source code
load_xtable Source code
makeFunctionalPrediction Source code
make_ecpdlist Source code
my.16sfun.anot Source code
my.corr.net Source code
my.fast.spar Source code
my.json.scatter Source code
my.json.scatter.pair Source code
my.pcoa.3d Source code
my.reduce.dimension Source code
my.secom.anal Source code
my.sparcc.net Source code
myFastList Source code
mz_tolerance Source code
overlap_ratio Source code
parse_taxonomy_silva_128 Source code
performPeakEnrich Source code
plotSeqDiagnotics Source code
plot_core Source code
prevalence Source code
prevalence_nsamples Source code
print_glm_stats Source code
qc.boxplot2 Source code
qc.pcaplot2 Source code
readDataQs Source code
readDataset Source code
readSet Source code
read_seq_len Source code
recordEnrTable Source code
rescale2NewRange Source code
residuals_plot Source code
rgba_to_hex_opacity Source code
rowcolFt Source code
rowcoltt Source code
runRefBlast Source code
s_diff_est Source code
saveDataQs Source code
saveSet Source code
scale_colours Source code
scale_mat Source code
scale_range Source code
scale_rows Source code
scale_vec_colours Source code
setIncludeMeta Source code
simpleCap Source code
sparse_dist Source code
sparse_linear Source code
subsetPhyloseqByDataset Source code
summaryRes Source code
sweaveBash4exec Source code
sweaveBash4execPro Source code
sweaveRScript4exec Source code
tr Source code
unitAutoScale Source code
validate_fastq Source code
xia-lab/MicrobiomeAnalystR documentation built on Sept. 7, 2024, 1:26 p.m.