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 |