Package: zitools 1.1.0
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:
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zitools.pdf |zitools.html✨
zitools/json (API)
NEWS
| # Install 'zitools' in R: |
| install.packages('zitools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kreutz-lab/zitools/issues
- mtx - Matrix Data
On BioConductor:zitools-1.1.0(bioc 3.21)zitools-1.0.0(bioc 3.20)
softwarestatisticalmethodmicrobiome
Last updated 2 months agofrom:9887f7da3b. Checks:OK: 1 WARNING: 4 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | WARNING | Nov 30 2024 |
| R-4.5-linux | WARNING | Nov 30 2024 |
| R-4.4-win | WARNING | Nov 30 2024 |
| R-4.4-mac | WARNING | Nov 30 2024 |
| R-4.3-win | NOTE | Sep 12 2024 |
| R-4.3-mac | NOTE | Sep 12 2024 |
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 page | Topics |
|---|---|
| Arithmetic Operators | * *,Zi,ANY-method |
| Arithmetic Operators | / /,Zi,ANY-method |
| Arithmetic Operators | + +,Zi,ANY-method -,Zi,ANY-method ´-´ |
| Access assays | assays assays,Zi-method |
| Create boxplots of a 'Zi'-class object | boxplot boxplot.Zi |
| Access the col Data | colData colData,Zi-method |
| Calculate the row or column means of zero-inflated count data | colMeans2 colMeans2,Zi-method rowMeans2 rowMeans2,Zi-method |
| Calculate the row or column median of zero-deinflated count data | colMedians colMedians,Zi-method rowMedians rowMedians,Zi-method |
| Calculate weighted Pearson Correlation coeffiecients | cor cor,Zi,ANY-method |
| Calculate weighted Covariance | cov cov,Zi,ANY-method |
| Access the model | deinflatedcounts deinflatedcounts,Zi-method deinflatedcounts<- deinflatedcounts<-,Zi-method |
| Draw a Heat Map | heatmap heatmap.Zi |
| Access the inputcounts | inputcounts inputcounts,Zi-method inputcounts<- inputcounts<-,Zi-method |
| Access and Set the inputdata | inputdata inputdata,Zi-method inputdata<- inputdata<-,Zi-method |
| log(1+x) | log1p log1p,Zi-method |
| log2p(x+1) | log2p log2p,Zi-method |
| Arithmetic Mean | mean mean.Zi |
| Calculate the median of zero-deinflated count data | median median.Zi |
| Missing Value Heatmap | MissingValueHeatmap |
| Access the model | model model,Zi-method model<- model<-,Zi-method |
| Matrix Data | mtx |
| Access the otu table | otu_table otu_table,Zi-method |
| Plotting | plot plot,Zi,ANY-method |
| Calculate the quantiles of zero-deinflated count data | quantile quantile.Zi |
| Resample a 'Zi'-class object | resample_deinflatedcounts |
| Access the row data | rowData rowData,Zi-method |
| Calculate the row or column quantiles of zero-deinflated count data | colQuantiles colQuantiles,Zi-method rowQuantiles rowQuantiles,Zi-method |
| Row and Column Standard Deviations of zero inflated count data | colSds colSds,Zi-method rowSds rowSds,Zi-method |
| Row and Column Variances of zero inflated count data | colVars colVars,Zi-method rowVars rowVars,Zi-method |
| Row and Column weighted means of zero inflated count data | colWeightedMeans colWeightedMeans,Zi-method rowWeightedMeans rowWeightedMeans,Zi-method |
| Row and column weighted standard deviations or variances of zero inflated count data | colWeightedSds colWeightedSds,Zi-method colWeightedVars colWeightedVars,Zi-method rowWeightedSds rowWeightedSds,Zi-method rowWeightedVars rowWeightedVars,Zi-method |
| Access the sample data | sample_data sample_data,Zi-method |
| Standard Deviation of zero inflated count data | sd sd,Zi-method |
| Show summary of Zi object | show show,Zi-method |
| Subset a 'Zi'-class object based on feature data | subset_feature |
| Subset a 'Zi'-class object based on sample data | subset_sample |
| Transpose a 'Zi'-class object | t t,Zi-method |
| Access the taxonomy table | tax_table tax_table,Zi-method |
| Variance of zero inflated count data | var var,Zi,ANY-method |
| Weighted Arithmetic Mean of zero inflated count data | weighted.mean weighted.mean,Zi-method |
| Weighted Variance and weighted Standard Deviation | weightedSd weightedSd,Zi-method weightedVar weightedVar,Zi-method |
| Access the weights | weights weights,Zi-method weights<- weights<-,Zi-method |
| Class Zi | Zi-class |
| Convert a 'Zi'-class object to a DESeq2 dds object | zi2deseq2 |
| Replace the otu table of a phyloseq object | zi2phyloseq |
| ziMain - main function to fit a zero inflation model and calculate weights for structural zeros | ziMain ziMain,phyloseq-method ziMain,SummarizedExperiment-method |
