Package: zitools 0.99.3

Carlotta Meyring

zitools: Analysis of zero-inflated count data

zitools allows for zero inflated count data analysis by either using down-weighting of excess zeros or by replacing an appropriate proportion of excess zeros with NA. Through overloading frequently used statistical functions (such as mean, median, standard deviation), plotting functions (such as boxplots or heatmap) or differential abundance tests, it allows a wide range of downstream analyses for zero-inflated data in a less biased manner. This becomes applicable in the context of microbiome analyses, where the data is often overdispersed and zero-inflated, therefore making data analysis extremly challenging.

Authors:Carlotta Meyring [aut, cre]

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NEWS

# Install 'zitools' in R:
install.packages('zitools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/kreutz-lab/zitools/issues

Datasets:
  • mtx - Matrix Data

On BioConductor:zitools-0.99.3(bioc 3.20)

bioconductor-package

51 exports 1.38 score 97 dependencies

Last updated 3 months agofrom:5f45d497cc

Exports:assayscolDatacolMeans2colMedianscolQuantilescolSdscolVarscolWeightedMeanscolWeightedSdscolWeightedVarscorcovdeinflatedcountsdeinflatedcounts<-heatmapinputcountsinputcounts<-inputdatainputdata<-log2pMissingValueHeatmapmodelmodel<-otu_tableplotresample_deinflatedcountsrowDatarowMeans2rowMediansrowQuantilesrowSdsrowVarsrowWeightedMeansrowWeightedSdsrowWeightedVarssample_datasdshowsubset_featuresubset_samplettax_tablevarweighted.meanweightedSdweightedVarweightsweights<-zi2deseq2zi2phyloseqziMain

Dependencies:abindade4apeaskpassBHBiobaseBiocGenericsBiocParallelbiomformatBiostringscliclustercodetoolscolorspacecpp11crayoncurldata.tableDelayedArrayDESeq2digestdplyrfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrigraphIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemulttestmunsellnlmeopensslpermutephyloseqpillarpixmappkgconfigplyrpsclpurrrR6RColorBrewerRcppRcppArmadilloreshape2rhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorsscalessnowspSparseArraystringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsveganVGAMviridisLitewithrXVectorzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Arithmetic Operators* *,Zi,ANY-method
Arithmetic Operators/ /,Zi,ANY-method
Arithmetic Operators+ +,Zi,ANY-method -,Zi,ANY-method ´-´
Access assaysassays assays,Zi-method
Create boxplots of a 'Zi'-class objectboxplot boxplot.Zi
Access the col DatacolData colData,Zi-method
Calculate the row or column means of zero-inflated count datacolMeans2 colMeans2,Zi-method rowMeans2 rowMeans2,Zi-method
Calculate the row or column median of zero-deinflated count datacolMedians colMedians,Zi-method rowMedians rowMedians,Zi-method
Calculate weighted Pearson Correlation coeffiecientscor cor,Zi,ANY-method
Calculate weighted Covariancecov cov,Zi,ANY-method
Access the modeldeinflatedcounts deinflatedcounts,Zi-method deinflatedcounts<- deinflatedcounts<-,Zi-method
Draw a Heat Mapheatmap heatmap.Zi
Access the inputcountsinputcounts inputcounts,Zi-method inputcounts<- inputcounts<-,Zi-method
Access and Set the inputdatainputdata inputdata,Zi-method inputdata<- inputdata<-,Zi-method
log(1+x)log1p log1p,Zi-method
log2p(x+1)log2p log2p,Zi-method
Arithmetic Meanmean mean.Zi
Calculate the median of zero-deinflated count datamedian median.Zi
Missing Value HeatmapMissingValueHeatmap
Access the modelmodel model,Zi-method model<- model<-,Zi-method
Matrix Datamtx
Access the otu tableotu_table otu_table,Zi-method
Plottingplot plot,Zi,ANY-method
Calculate the quantiles of zero-deinflated count dataquantile quantile.Zi
Resample a 'Zi'-class objectresample_deinflatedcounts
Access the row datarowData rowData,Zi-method
Calculate the row or column quantiles of zero-deinflated count datacolQuantiles colQuantiles,Zi-method rowQuantiles rowQuantiles,Zi-method
Row and Column Standard Deviations of zero inflated count datacolSds colSds,Zi-method rowSds rowSds,Zi-method
Row and Column Variances of zero inflated count datacolVars colVars,Zi-method rowVars rowVars,Zi-method
Row and Column weighted means of zero inflated count datacolWeightedMeans colWeightedMeans,Zi-method rowWeightedMeans rowWeightedMeans,Zi-method
Row and column weighted standard deviations or variances of zero inflated count datacolWeightedSds colWeightedSds,Zi-method colWeightedVars colWeightedVars,Zi-method rowWeightedSds rowWeightedSds,Zi-method rowWeightedVars rowWeightedVars,Zi-method
Access the sample datasample_data sample_data,Zi-method
Standard Deviation of zero inflated count datasd sd,Zi-method
Show summary of Zi objectshow show,Zi-method
Subset a 'Zi'-class object based on feature datasubset_feature
Subset a 'Zi'-class object based on sample datasubset_sample
Transpose a 'Zi'-class objectt t,Zi-method
Access the taxonomy tabletax_table tax_table,Zi-method
Variance of zero inflated count datavar var,Zi,ANY-method
Weighted Arithmetic Mean of zero inflated count dataweighted.mean weighted.mean,Zi-method
Weighted Variance and weighted Standard DeviationweightedSd weightedSd,Zi-method weightedVar weightedVar,Zi-method
Access the weightsweights weights,Zi-method weights<- weights<-,Zi-method
Class ZiZi-class
Convert a 'Zi'-class object to a DESeq2 dds objectzi2deseq2
Replace the otu table of a phyloseq objectzi2phyloseq
ziMain - main function to fit a zero inflation model and calculate weights for structural zerosziMain ziMain,phyloseq-method ziMain,SummarizedExperiment-method