Package index • gnomeR

Processing Data

create_gene_binary(): Enables creation of a binary matrix from a mutation, fusion or CNA file with a predefined list of samples (rows are samples and columns are genes)

summarize_by_gene(): Simplify binary matrix to one column per gene that counts any alteration type as 1

summarize_by_patient(): Simplify binary matrix to one column per patient that counts any alteration type across all samples as 1

pivot_cna_wider(): Pivot CNA from maf (long) version to wide version

pivot_cna_longer(): Reformat Wide CNA Data to Long

add_pathways(): Pathway Alterations

recode_alias(): Recode Hugo Symbol Column

reformat_fusion(): Enables users to reformat fusions files so that each fusion is listed as one row with two hugo-symbol sites instead of two rows, one for each site. This is the required format for the create_gene_binary function.

subset_by_panel(): Subset a Binary Matrix By Genes Available on Specified Panel

Analyzing Data

tbl_genomic(): tbl_genomic

mutation_viz(): Creates a set of plot summarising a mutation file.

ggvarclass(): Barplot of Variant Classification Counts

ggvartype(): Barplot of Variant Type Counts

ggsamplevar(): #' Utility Function to Extract SNV #' #' @param x string #' @param n number of characters from right #' #' @return string #' @noRd #' @examples #' substrRight("Hello", 2) #' substrRight <- function(x, n) x <- as.character(x) substr(x, nchar(x) - n + 1, nchar(x)) Histogram of Variants Per Sample Colored By Variant Classification

ggtopgenes(): Barplot of Most Frequently Altered Genes

gggenecor(): Correlation Heatmap of the Top Altered Genes

ggcomut(): Comutation Heatmap of the Top Altered Genes

subset_by_frequency(): Subset a Binary Matrix By Alteration Frequency Threshold

Helper Functions

which_impact_panel(): provide a list of impact panels a provided gene is found within

recode_cna(): Function to recode numeric CNA alteration values to factor values

rename_columns(): Rename columns from API results to work with gnomeR functions

resolve_alias(): Resolve Hugo Symbol Names with Aliases

extract_patient_id(): Extract IMPACT Patient ID From Sample ID

Color Palette

gnomer_colors: List of suggested color palettes for when you need a large palette

gnomer_palettes: Complete list of gnomeR color palettes

gnomer_palette(): Access the colors in a gnomeR color palette

set_gnomer_palette(): Set gnomeR color palette

reset_gnomer_palette(): Reset gnomeR color palette

Example Data Sets

mutations: An example IMPACT cBioPortal mutation data set in API format

cna: An example IMPACT cBioPortal mutation data set in API format

sv: An example IMPACT cBioPortal mutation data set in API format

seg: A segmentation file from the cbioPortal datasets

cna_wide: An example IMPACT cBioPortal CNA in wide format

consequence_map: Consequence Map

gene_panels: Public Gene Panels on cBioPortal

names_df: Data Frame of Column Names

pathways: IMPACT Oncogenic Signaling Pathways

impact_alias_table: IMPACT Alias Tables

genie_alias_table: GENIE Alias Table

sv_long: An example of long-format fusion/sv files

clin_collab_df: An example data set for an IMPACT analysis coming from a clinical collaborator

genie_mut: An example GENIE BPC mutations data set

genie_cna: An example GENIE BPC CNA data set

genie_fusion: An example GENIE BPC fusions data set