Man pages for AxelitoMartin/gnomeR
Wrangle and analyze IMPACT and TCGA mutation data

add_pathwaysPathway Alterations
add.percAdd a percentage to counts
annotate_any_panelAnnotate Missing Gene Values According to Specifi Panels
annotate_specific_panelUtility function to insert NA's According to Panel
check_cna_inputCheck CNA data frame to ensure columns are correct
check_fusion_inputCheck fusion data frame to ensure columns are correct
check_mutation_inputChecks MAF input to ensure column names are correct and...
clin.patientsAn example of clinical patient level information file from...
clin.sampleAn example of clinical sample level information file from...
cnaAn example copy number alteration raw calls file from IMPACT...
CNregions.modCNregions.mod Modified CNregions function from the facets...
create_gene_binaryEnables creation of a binary matrix from a mutation file with...
curated_genesList of curated genes for IMPACT oncoKB annotation.
dat_oncoprintEnables creation of a matrix used to generate an OncoPrint...
dot-cna_gene_binaryMake Binary Matrix From CNA data frame
dot-fusions_gene_binaryMake Binary Matrix From Fusion data frame
dot-mutations_gene_binaryMake Binary Matrix From Mutation data frame
dot-sum_alts_in_pathwayTitle
facets_datfacets_dat
facets_heatmapfacets_heatmap
fusionAn example of fusions calls file from IMPACT cbioPortal...
gene_panelsPublic Gene Panels on cBioPortal
genie_gene_infoGENIE consortium Gene Meta Data
ggcomutComutation Heatmap of the Top Altered Genes
gggenecorCorrelation Heatmap of the Top Altered Genes
ggheatmapHeatmap of all events after gene_binary - using binary...
ggsamplevarHistogram of Variants Per Sample Colored By Variant...
ggsnvclassHistogram of SNV class Counts
ggtopgenesBarplot of Most Frequently Altered Genes
ggvarclassBarplot of Variant Classification Counts
ggvartypeBarplot of Variant Type Counts
gnomer_colorsList of suggested color palettes for when you need a large...
gnomer_colsFunction to extract colors from 'gnomer_colors' as hex codes
gnomeR-packagegnomeR: Wrangle and analyze IMPACT and TCGA mutation data
gnomer_palReturn function to interpolate a gnomeR color palette
gnomer_paletteAccess the colors in a gnomeR color palette
gnomer_palettesComplete list of gnomeR color palettes
impact_gene_infoIMPACT Gene Meta Data
mutAn example maf file from IMPACT cbioPortal dataset
mutation_vizCreates a set of plot summarising a mutation file.
oncokbOncoKB annotate \ Enables oncokb annotation of MAF, fusions...
panel_namesGENIE panel names as found in synapse data
pathwaysIMPACT Gene Pathways
pipePipe operator
plot_oncoprintCreates the OncoPrint corresponding to the inputted genetic...
recode_aliasRecode Hugo Symbol Column
reformat_cnaReformat CNA from maf version to wide version
resolve_aliasResolve Hugo Symbol Names with Aliases
scale_color_pancanColor scale creator to add gnomeR colors in ggplot
scale_fill_pancanFill scale creator to add gnomeR colors in ggplot
segA segmentation file from the cbioPortal datasets
specify_impact_panelsIMPACT Panel Annotation of NA's
substrRightUtility Function to Extract SNV
summarize_by_geneSimplify binary matrix to one column per gene that counts any...
tbl_genomictbl_genomic
tcga_genesA vector of 19441 hugo symbols in TCGA
tcga_samplesData frame of all TCGA sample ids and their corresponding...
ti_341Intervals sequenced in 341 panel
ti_410Intervals sequenced in 410 panel
ti_468Intervals sequenced in 468 panel
AxelitoMartin/gnomeR documentation built on April 21, 2022, 3:01 p.m.