Man pages for hcnh174/hlsgr
Hiroshima Liver Study Group R Utilities
| addIdColumn | Add rowname as a column |
| analyzeSalmonDataDeSeq2 | Analyze Salmon quant data using DeSeq2 |
| analyzeSalmonDeSeq2 | Analyze Salmon quant data using DeSeq2 |
| appendValues | Append values to vector |
| checkColExists | Throws an error if a column does not exist in a dataframe |
| checkFileExists | Title |
| colExists | Checks if a column exists in a dataframe |
| concat | Concatenate strings similar to paste0 |
| containsElement | Checks if a vector contains a value |
| DeSeq2Class | R6 class for DESeq2 analysis |
| EdgeRClass | R6 class for EdgeR analysis |
| excludeColumns | Exclude columns from dataframe |
| getCountsByGroup | getCountsByGroup adjusts the counts and samples to exclude... |
| getGroupLevels | getGroupLevels returns uniquq ordered levels for specified... |
| getSamplesByGroup | getSamplesByGroup |
| hasColumn | Checks if a dataframe has a column |
| hlsgr | hlsgr: bioinformatics and genomics utilities for HLSG |
| HmtMetabolomicsDataClass | R6 class for HMT metabolomics data |
| LimmaVoomClass | R6 class for limma voom analysis |
| loadDataFrame | Load data frame |
| loadGroups | loadGroups |
| loadNgsProject | Load NGS project metadata from dir |
| loadRuns | loadRuns |
| loadSalmonData | Load Salmon quant files |
| loadSalmonSamples | Load sample information for Salmon-mapped samples |
| loadSamples | Load sample information |
| loadSubjects | loadSubjects |
| loadSubreadData | Load Subread count files |
| lookupGenes | Return a vector gene names corresponding to a vector of... |
| makeDeSeq2Table | Create a formatted table of differentially regulated genes |
| MetaboAnalystClass | R6 class for MetaboAnalyst analysis |
| MetaboDiffClass | R6 class for MetaboDiff analysis |
| MixomicsClass | R6 class for mixomics analysis |
| NgsProjectClass | R6 class for project information |
| pipe | Pipe operator |
| plotChromosomes | Create a circular chromsome plot showing location of variants |
| plotDeSeq2Heatmap | Create a heatmap for DeSeq2 RNASeq data |
| plotKeggPathway | Title |
| readSalmonData | Read Salmon data from RDS file |
| removeElements | Remove elements from vector |
| RnaSeqCountDataClass | R6 class to provide a common interface for count data |
| RoplsClass | R6 class for RoplsClass analysis |
| SalmonClass | R6 class for importing salmon count data |
| saveSalmonData | Write Salmon quant data to to rds file for faster loading... |
| splitFields | Split fields on delimiter |
| splitGenes | Split list of genes into a vector |
| subsetTxi | Subset txi data by sample or gene |
| TakedaMetabolomicsDataClass | R6 class for Takeda metabolomics data |
| trim | Trims whitespace from string |
| WgcnaClass | create R6 class method for WGCNA |
| writeTable | Write table to file |
