Analysis of zero-inflated count data

Documentation for package ‘zitools’ version 1.3.0

Help Pages

-- 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