Man pages for PathoStat
PathoStat Statistical Microbiome Analysis Package

Bootstrap_LOOCV_LR_AUCDo bootstrap and LOOCV
Chisq_Test_PamGiven PAM and disease/control annotation, do Chi-square test...
findRAfromCountReturn the Relative Abundance (RA) data for the given count...
findTaxonMatFind the Taxonomy Information Matrix
findTaxonomyFind the taxonomy for unlimited tids
findTaxonomy300Find the taxonomy for maximum 300 tids
Fisher_Test_PamGiven PAM and disease/control annotation, do Chi-square test...
formatTaxTableFormat taxonomy table for rendering
GET_PAMtransform cpm counts to presence-absence matrix
getShinyInputGetter function to get the shinyInput option
getShinyInputCombatGetter function to get the shinyInputCombat option
getShinyInputOrigGetter function to get the shinyInputOrig option
getSignatureFromMultipleGlmnetUse Lasso to do feature selection
grepTidGreps the tid from the given identifier string
loadPathoscopeReportsLoads all data from a set of PathoID reports. For each column...
loadPstatLoad the R data(.rda) file with pathostat object
log2CPMCompute log2(counts per mil reads) and library size for each...
LOOAUC_simple_multiple_noplot_one_dfLOOCV
LOOAUC_simple_multiple_one_dfLOOCV with ROC curve
PathoStat-classPathoStat class to store PathoStat input data including...
percentCompute percentage
phyloseq_to_edgeRConvert phyloseq OTU count data into DGEList for edgeR...
plotPCAPlotlyPlot PCA
plotPCoAPlotlyPlot PCoA
pstat_datapathostat object generated from example pathoscope report...
readPathoscopeDataReads the data from PathoScope reports and returns a list of...
runPathoStatStatistical Microbiome Analysis on the pathostat input and...
savePstatSave the pathostat object to R data(.rda) file
setShinyInputSetter function to set the shinyInput option
setShinyInputCombatSetter function to set the shinyInputCombat option
setShinyInputOrigSetter function to set the shinyInputOrig option
summarizeTableSummarize sample
TranslateIdToTaxLevelFind the taxonomy for the given taxon id name
Wilcox_Test_dfMann-whitney test for a dataframe
PathoStat documentation built on Dec. 3, 2018, 6 p.m.