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 |