PathoStat Statistical Microbiome Analysis Package

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Documentation for package ‘PathoStat’ version 1.33.0

• 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