# PathoStat Statistical Microbiome Analysis Package

## Documentation for package ‘PathoStat’ version 1.12.0

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

## Help Pages

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
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
GET_PAM | transform cpm counts to presence-absence 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
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
pathostat1 | 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 | 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
summarizeTable | Summarize sample
TranslateIdToTaxLevel | Find the taxonomy for the given taxon id name
Wilcox_Test_df | Mann-whitney test for a dataframe