# Analysis of zero-inflated count data

## Documentation for package ‘zitools’ version 1.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D H I L M O P Q R S T V W Z misc

## -- A --

assays | Access assays
assays-method | Access assays

## -- B --

boxplot | Create boxplots of a 'Zi'-class object
boxplot.Zi | Create boxplots of a 'Zi'-class object

## -- C --

colData | Access the col Data
colData-method | Access the col Data
colMeans2 | Calculate the row or column means of zero-inflated count data
colMeans2-method | Calculate the row or column means of zero-inflated count data
colMedians | Calculate the row or column median of zero-deinflated count data
colMedians-method | Calculate the row or column median of zero-deinflated count data
colQuantiles | Calculate the row or column quantiles of zero-deinflated count data
colQuantiles-method | Calculate the row or column quantiles of zero-deinflated count data
colSds | Row and Column Standard Deviations of zero inflated count data
colSds-method | Row and Column Standard Deviations of zero inflated count data
colVars | Row and Column Variances of zero inflated count data
colVars-method | Row and Column Variances of zero inflated count data
colWeightedMeans | Row and Column weighted means of zero inflated count data
colWeightedMeans-method | Row and Column weighted means of zero inflated count data
colWeightedSds | Row and column weighted standard deviations or variances of zero inflated count data
colWeightedSds-method | Row and column weighted standard deviations or variances of zero inflated count data
colWeightedVars | Row and column weighted standard deviations or variances of zero inflated count data
colWeightedVars-method | Row and column weighted standard deviations or variances of zero inflated count data
cor | Calculate weighted Pearson Correlation coeffiecients
cor-method | Calculate weighted Pearson Correlation coeffiecients
cov | Calculate weighted Covariance
cov-method | Calculate weighted Covariance

## -- D --

deinflatedcounts | Access the model
deinflatedcounts-method | Access the model
deinflatedcounts<- | Access the model
deinflatedcounts<--method | Access the model

## -- H --

heatmap | Draw a Heat Map
heatmap.Zi | Draw a Heat Map

## -- I --

inputcounts | Access the inputcounts
inputcounts-method | Access the inputcounts
inputcounts<- | Access the inputcounts
inputcounts<--method | Access the inputcounts
inputdata | Access and Set the inputdata
inputdata-method | Access and Set the inputdata
inputdata<- | Access and Set the inputdata
inputdata<--method | Access and Set the inputdata

## -- L --

log1p | log(1+x)
log1p-method | log(1+x)
log2p | log2p(x+1)
log2p-method | log2p(x+1)

## -- M --

mean | Arithmetic Mean
mean.Zi | Arithmetic Mean
median | Calculate the median of zero-deinflated count data
median.Zi | Calculate the median of zero-deinflated count data
MissingValueHeatmap | Missing Value Heatmap
model | Access the model
model-method | Access the model
model<- | Access the model
model<--method | Access the model
mtx | Matrix Data

## -- O --

otu_table | Access the otu table
otu_table-method | Access the otu table

## -- P --

plot | Plotting
plot-method | Plotting

## -- Q --

quantile | Calculate the quantiles of zero-deinflated count data
quantile.Zi | Calculate the quantiles of zero-deinflated count data

## -- R --

resample_deinflatedcounts | Resample a 'Zi'-class object
rowData | Access the row data
rowData-method | Access the row data
rowMeans2 | Calculate the row or column means of zero-inflated count data
rowMeans2-method | Calculate the row or column means of zero-inflated count data
rowMedians | Calculate the row or column median of zero-deinflated count data
rowMedians-method | Calculate the row or column median of zero-deinflated count data
rowQuantiles | Calculate the row or column quantiles of zero-deinflated count data
rowQuantiles-method | Calculate the row or column quantiles of zero-deinflated count data
rowSds | Row and Column Standard Deviations of zero inflated count data
rowSds-method | Row and Column Standard Deviations of zero inflated count data
rowVars | Row and Column Variances of zero inflated count data
rowVars-method | Row and Column Variances of zero inflated count data
rowWeightedMeans | Row and Column weighted means of zero inflated count data
rowWeightedMeans-method | Row and Column weighted means of zero inflated count data
rowWeightedSds | Row and column weighted standard deviations or variances of zero inflated count data
rowWeightedSds-method | Row and column weighted standard deviations or variances of zero inflated count data
rowWeightedVars | Row and column weighted standard deviations or variances of zero inflated count data
rowWeightedVars-method | Row and column weighted standard deviations or variances of zero inflated count data

## -- S --

sample_data | Access the sample data
sample_data-method | Access the sample data
sd | Standard Deviation of zero inflated count data
sd-method | Standard Deviation of zero inflated count data
show | Show summary of Zi object
show-method | Show summary of Zi object
subset_feature | Subset a 'Zi'-class object based on feature data
subset_sample | Subset a 'Zi'-class object based on sample data

## -- T --

t | Transpose a 'Zi'-class object
t-method | Transpose a 'Zi'-class object
tax_table | Access the taxonomy table
tax_table-method | Access the taxonomy table

## -- V --

var | Variance of zero inflated count data
var-method | Variance of zero inflated count data

## -- W --

weighted.mean | Weighted Arithmetic Mean of zero inflated count data
weighted.mean-method | Weighted Arithmetic Mean of zero inflated count data
weightedSd | Weighted Variance and weighted Standard Deviation
weightedSd-method | Weighted Variance and weighted Standard Deviation
weightedVar | Weighted Variance and weighted Standard Deviation
weightedVar-method | Weighted Variance and weighted Standard Deviation
weights | Access the weights
weights-method | Access the weights
weights<- | Access the weights
weights<--method | Access the weights

## -- Z --

Zi-class | Class Zi
zi2deseq2 | Convert a 'Zi'-class object to a DESeq2 dds object
zi2phyloseq | Replace the otu table of a phyloseq object
ziMain | ziMain - main function to fit a zero inflation model and calculate weights for structural zeros
ziMain-method | ziMain - main function to fit a zero inflation model and calculate weights for structural zeros

## -- misc --

* | Arithmetic Operators
*-method | Arithmetic Operators
+ | Arithmetic Operators
+-method | Arithmetic Operators
--method | Arithmetic Operators
/ | Arithmetic Operators
/-method | Arithmetic Operators
´-´ | Arithmetic Operators