PathoStat Statistical Microbiome Analysis Package

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Documentation for package ‘PathoStat’ version 1.2.1

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coreOTU Compute Core OTUs for the given data matrix
coreOTUModule Server function for Core OTU Module
coreOTUModuleUI UI function for Core OTU Module
coreOTUNormalize Compute Empirical Bayes OTU Normalized data
coreOTUQuantile Compute coreOTU Quantile Normalized data
createPathoStat Generates a PathoStat object from the PathoScope reports for further analysis using the interactive shiny app
findRAfromCount Return the Relative Abundance (RA) data for the given count OTU table
findTaxonLevel Find the taxonomy for the given taxon id
findTaxonMat Find the Taxonomy Information Matrix
findTaxonomy Find the taxonomy for each taxon ids
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
get_core Select rows of OTU matrix that meet given detection and prevalence thresholds
get_coremat Create core OTU matrix containing number of OTUs detected at varying detection and prevalence thresholds.
get_coremat_lineplot Create line plot from core OTU 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
pathostat Build PathoStat-class object from its phyloseq component.
PathoStat-class PathoStat class to store PathoStat input data including phyloseq object
pathostat1 PathoStat class to store PathoStat input data including phyloseq object
plotConfRegion Compute the confidence region for the given proportions
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
sizeNormalize Normalize the given data based on library size