# PathoStat Statistical Microbiome Analysis Package

## Documentation for package ‘PathoStat’ version 1.4.1

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

## Help Pages

coreOTU | Compute Core OTUs for the given data matrix
coreOTUModule | Server function for Core OTU Module
coreOTUModuleUI | UI function for Core OTU Module
coreOTUNormalize | Compute Empirical Bayes OTU Normalized data
coreOTUQuantile | Compute coreOTU Quantile Normalized data
createPathoStat | Generates a PathoStat object from the PathoScope reports for further analysis using the interactive shiny app
findRAfromCount | Return the Relative Abundance (RA) data for the given count OTU table
findTaxonLevel | Find the taxonomy for the given taxon id
findTaxonMat | Find the Taxonomy Information Matrix
findTaxonomy | Find the taxonomy for each taxon ids
formatTaxTable | Format taxonomy table for rendering
getShinyInput | Getter function to get the shinyInput option
getShinyInputCombat | Getter function to get the shinyInputCombat option
getShinyInputOrig | Getter function to get the shinyInputOrig option
get_core | Select rows of OTU matrix that meet given detection and prevalence thresholds
get_coremat | Create core OTU matrix containing number of OTUs detected at varying detection and prevalence thresholds.
get_coremat_lineplot | Create line plot from core OTU matrix
grepTid | Greps the tid from the given identifier string
loadPathoscopeReports | Loads all data from a set of PathoID reports. For each column in the PathoID report, construct a matrix where the rows are genomes and the columns are samples. Returns a list where each element is named according to the PathoID column. For example, ret[["Final.Best.Hit.Read.Numbers"]] on the result of this function will get you the final count matrix. Also includes elements "total_reads" and "total_genomes" from the first line of the PathoID report.
loadPstat | Load the R data(.rda) file with pathostat object
log2CPM | Compute log2(counts per mil reads) and library size for each sample
pathostat | Build PathoStat-class object from its phyloseq component.
PathoStat-class | PathoStat class to store PathoStat input data including phyloseq object
pathostat1 | PathoStat class to store PathoStat input data including phyloseq object
plotConfRegion | Compute the confidence region for the given proportions
pstat | pathostat object generated from example pathoscope report files
pstat_data | pathostat object generated from example pathoscope report files
readPathoscopeData | Reads the data from PathoScope reports and returns a list of final guess relative abundance and count data
runPathoStat | Statistical Microbiome Analysis on the pathostat input and generates a html report and produces interactive shiny app plots
savePstat | Save the pathostat object to R data(.rda) file
setShinyInput | Setter function to set the shinyInput option
setShinyInputCombat | Setter function to set the shinyInputCombat option
setShinyInputOrig | Setter function to set the shinyInputOrig option
sizeNormalize | Normalize the given data based on library size