PathoStat-class         PathoStat class to store PathoStat input data
                        including phyloseq object
coreOTUModule           Server function for Core OTU Module
coreOTUModuleUI         UI function for Core OTU Module
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.
plotConfRegion          Compute the confidence region for the given
                        proportions
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
