Man pages for MSKCC-Epi-Bio/gnomeR
Wrangle and analyze IMPACT and TCGA mutation data
| add_pathways | Pathway Alterations |
| annotate_any_panel | Annotate Missing Gene Values According to Specific Panels |
| annotate_specific_panel | Utility function to insert NA's According to Panel |
| clin_collab_df | An example data set for an IMPACT analysis coming from a... |
| cna | An example IMPACT cBioPortal mutation data set in API format |
| cna_wide | An example IMPACT cBioPortal CNA in wide format |
| consequence_map | Consequence Map |
| create_gene_binary | Enables creation of a binary matrix from a mutation, fusion... |
| dot-abort_if_not_numeric | Check if all gene_binary columns except sample_id and... |
| dot-check_for_fus_in_mut | Check for fusions in maf file |
| dot-check_for_silent | Check for silent mutations |
| dot-check_required_cols | Check a Data Frame for Required Columns |
| dot-clean_and_check_cols | Checks genomic input file columns to ensure column names are... |
| dot-cna_gene_binary | Make Binary Matrix From CNA data frame |
| dot-filter_to_sample_list | Filter to final sample list |
| dot-fusions_gene_binary | Make Binary Matrix From Fusion data frame |
| dot-infer_mutation_status | Infer mutation status and assume somatic if none |
| dot-infer_variant_type | Infer variant type if not present in data |
| dot-mutations_gene_binary | Make Binary Matrix From Mutation data frame |
| dot-paste_endings | Add descriptive endings to hugo symbol names that do not have... |
| dot-process_binary | Create binary data.frames depending on type of mutation data |
| dot-sum_alts_in_pathway | Sum Alterations in a Pathway |
| extract_patient_id | Extract IMPACT Patient ID From Sample ID |
| gene_panels | Public Gene Panels on cBioPortal |
| genie_alias_table | GENIE Alias Table |
| genie_cna | An example GENIE BPC CNA data set |
| genie_fusion | An example GENIE BPC fusions data set |
| genie_mut | An example GENIE BPC mutations data set |
| ggcomut | Comutation Heatmap of the Top Altered Genes |
| gggenecor | Correlation Heatmap of the Top Altered Genes |
| ggsamplevar | #' Utility Function to Extract SNV #' #' @param x string #'... |
| ggtopgenes | Barplot of Most Frequently Altered Genes |
| ggvarclass | Barplot of Variant Classification Counts |
| ggvartype | Barplot of Variant Type Counts |
| gnomer_colors | List of suggested color palettes for when you need a large... |
| gnomeR-package | gnomeR: Wrangle and analyze IMPACT and TCGA mutation data |
| gnomer_palette | Access the colors in a gnomeR color palette |
| gnomer_palettes | Complete list of gnomeR color palettes |
| impact_alias_table | IMPACT Alias Tables |
| mutations | An example IMPACT cBioPortal mutation data set in API format |
| mutation_viz | Creates a set of plot summarising a mutation file. |
| names_df | Data Frame of Column Names |
| pathways | IMPACT Oncogenic Signaling Pathways |
| pivot_cna_longer | Reformat Wide CNA Data to Long |
| pivot_cna_wider | Pivot CNA from maf (long) version to wide version |
| recode_alias | Recode Hugo Symbol Column |
| recode_cna | Function to recode numeric CNA alteration values to factor... |
| reexports | Objects exported from other packages |
| reformat_fusion | Enables users to reformat fusions files so that each fusion... |
| rename_columns | Rename columns from API results to work with gnomeR functions |
| reset_gnomer_palette | Reset gnomeR color palette |
| resolve_alias | Resolve Hugo Symbol Names with Aliases |
| seg | A segmentation file from the cbioPortal datasets |
| set_gnomer_palette | Set gnomeR color palette |
| specify_impact_panels | IMPACT Panel Annotation of NA's |
| subset_by_frequency | Subset a Binary Matrix By Alteration Frequency Threshold |
| subset_by_panel | Subset a Binary Matrix By Genes Available on Specified Panel |
| summarize_by_gene | Simplify binary matrix to one column per gene that counts any... |
| summarize_by_patient | Simplify binary matrix to one column per patient that counts... |
| sv | An example IMPACT cBioPortal mutation data set in API format |
| sv_long | An example of long-format fusion/sv files |
| tbl_genomic | tbl_genomic |
| which_impact_panel | provide a list of impact panels a provided gene is found... |
