Man pages for Bioconductor-mirror/PathoStat
PathoStat Statistical Microbiome Analysis Package

coreOTUCompute Core OTUs for the given data matrix
coreOTUModuleServer function for Core OTU Module
coreOTUModuleUIUI function for Core OTU Module
coreOTUNormalizeCompute Empirical Bayes OTU Normalized data
coreOTUQuantileCompute coreOTU Quantile Normalized data
createPathoStatGenerates a PathoStat object from the PathoScope reports for...
findRAfromCountReturn the Relative Abundance (RA) data for the given count...
findTaxonLevelFind the taxonomy for the given taxon id
findTaxonLevelDataFind the taxonomy level data for the given taxon level
findTaxonMatFind the Taxonomy Information Matrix
findTaxonomyFind the taxonomy for each taxon ids
formatTaxTableFormat taxonomy table for rendering
get_coreSelect rows of OTU matrix that meet given detection and...
get_corematCreate core OTU matrix containing number of OTUs detected at...
get_coremat_lineplotCreate line plot from core OTU matrix
getShinyInputGetter function to get the shinyInput option
getShinyInputCombatGetter function to get the shinyInputCombat option
getShinyInputOrigGetter function to get the shinyInputOrig option
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...
pathostatBuild PathoStat-class object from its phyloseq component.
PathoStat-classPathoStat class to store PathoStat input data including...
plotConfRegionCompute the confidence region for the given proportions
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
sizeNormalizeNormalize the given data based on library size
Bioconductor-mirror/PathoStat documentation built on May 31, 2017, 10:34 p.m.