Bootstrap_LOOCV_LR_AUC
                        Do bootstrap and LOOCV
Chisq_Test_Pam          Given PAM and disease/control annotation, do
                        Chi-square test for each row of PAM
findRAfromCount         Return the Relative Abundance (RA) data for the
                        given count OTU table
findTaxonMat            Find the Taxonomy Information Matrix
findTaxonomy            Find the taxonomy for unlimited tids
findTaxonomy300         Find the taxonomy for maximum 300 tids
Fisher_Test_Pam         Given PAM and disease/control annotation, do
                        Chi-square test for each row of PAM
formatTaxTable          Format taxonomy table for rendering
GET_PAM                 transform cpm counts to presence-absence matrix
getShinyInput           Getter function to get the shinyInput option
getShinyInputCombat     Getter function to get the shinyInputCombat
                        option
getShinyInputOrig       Getter function to get the shinyInputOrig
                        option
getSignatureFromMultipleGlmnet
                        Use Lasso to do feature selection
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
LOOAUC_simple_multiple_noplot_one_df
                        LOOCV
LOOAUC_simple_multiple_one_df
                        LOOCV with ROC curve
PathoStat-class         PathoStat class to store PathoStat input data
                        including phyloseq object
percent                 Compute percentage
phyloseq_to_edgeR       Convert phyloseq OTU count data into DGEList
                        for edgeR package
plotPCAPlotly           Plot PCA
plotPCoAPlotly          Plot PCoA
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
summarizeTable          Summarize sample
TranslateIdToTaxLevel   Find the taxonomy for the given taxon id name
Wilcox_Test_df          Mann-whitney test for a dataframe
