PathoStat Statistical Microbiome Analysis Package

[Up] [Top]

Documentation for package ‘PathoStat’ version 1.13.1

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