Man pages for AxelitoMartin/gnomeR
Wrangle and analyze IMPACT and TCGA mutation data
| add_pathways | Pathway Alterations |
| add.perc | Add a percentage to counts |
| annotate_any_panel | Annotate Missing Gene Values According to Specifi Panels |
| annotate_specific_panel | Utility function to insert NA's According to Panel |
| check_cna_input | Check CNA data frame to ensure columns are correct |
| check_fusion_input | Check fusion data frame to ensure columns are correct |
| check_mutation_input | Checks MAF input to ensure column names are correct and... |
| clin.patients | An example of clinical patient level information file from... |
| clin.sample | An example of clinical sample level information file from... |
| cna | An example copy number alteration raw calls file from IMPACT... |
| CNregions.mod | CNregions.mod Modified CNregions function from the facets... |
| create_gene_binary | Enables creation of a binary matrix from a mutation file with... |
| curated_genes | List of curated genes for IMPACT oncoKB annotation. |
| dat_oncoprint | Enables creation of a matrix used to generate an OncoPrint... |
| dot-cna_gene_binary | Make Binary Matrix From CNA data frame |
| dot-fusions_gene_binary | Make Binary Matrix From Fusion data frame |
| dot-mutations_gene_binary | Make Binary Matrix From Mutation data frame |
| dot-sum_alts_in_pathway | Title |
| facets_dat | facets_dat |
| facets_heatmap | facets_heatmap |
| fusion | An example of fusions calls file from IMPACT cbioPortal... |
| gene_panels | Public Gene Panels on cBioPortal |
| genie_gene_info | GENIE consortium Gene Meta Data |
| ggcomut | Comutation Heatmap of the Top Altered Genes |
| gggenecor | Correlation Heatmap of the Top Altered Genes |
| ggheatmap | Heatmap of all events after gene_binary - using binary... |
| ggsamplevar | Histogram of Variants Per Sample Colored By Variant... |
| ggsnvclass | Histogram of SNV class Counts |
| 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_cols | Function to extract colors from 'gnomer_colors' as hex codes |
| gnomeR-package | gnomeR: Wrangle and analyze IMPACT and TCGA mutation data |
| gnomer_pal | Return function to interpolate a gnomeR color palette |
| gnomer_palette | Access the colors in a gnomeR color palette |
| gnomer_palettes | Complete list of gnomeR color palettes |
| impact_gene_info | IMPACT Gene Meta Data |
| mut | An example maf file from IMPACT cbioPortal dataset |
| mutation_viz | Creates a set of plot summarising a mutation file. |
| oncokb | OncoKB annotate \ Enables oncokb annotation of MAF, fusions... |
| panel_names | GENIE panel names as found in synapse data |
| pathways | IMPACT Gene Pathways |
| pipe | Pipe operator |
| plot_oncoprint | Creates the OncoPrint corresponding to the inputted genetic... |
| recode_alias | Recode Hugo Symbol Column |
| reformat_cna | Reformat CNA from maf version to wide version |
| resolve_alias | Resolve Hugo Symbol Names with Aliases |
| scale_color_pancan | Color scale creator to add gnomeR colors in ggplot |
| scale_fill_pancan | Fill scale creator to add gnomeR colors in ggplot |
| seg | A segmentation file from the cbioPortal datasets |
| specify_impact_panels | IMPACT Panel Annotation of NA's |
| substrRight | Utility Function to Extract SNV |
| summarize_by_gene | Simplify binary matrix to one column per gene that counts any... |
| tbl_genomic | tbl_genomic |
| tcga_genes | A vector of 19441 hugo symbols in TCGA |
| tcga_samples | Data frame of all TCGA sample ids and their corresponding... |
| ti_341 | Intervals sequenced in 341 panel |
| ti_410 | Intervals sequenced in 410 panel |
| ti_468 | Intervals sequenced in 468 panel |
