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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
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()
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()
Internal 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