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| 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 |