|
CNregions.mod()
|
CNregions.mod
Modified CNregions function from the facets package to handle small sample sizes. |
|
binmat()
|
binmat
Enables creation of a binary matrix from a maf file with
a predefined list of patients (rows are patients and columns are genes) |
|
check_maf_column()
|
Check Columns of MAF |
|
check_maf_input()
|
Checks MAF input to ensure column names are correct and renamed genes are corrected |
|
clin.patients
|
An example of clinical patient level information file from
IMPACT cbioPortal dataset. |
|
clin.sample
|
An example of clinical sample level information file from IMPACT cbioPortal dataset. |
|
cna
|
An example copy number alteration raw calls file from IMPACT cbioPortal dataset |
|
curated_genes
|
List of curated genes for IMPACT oncoKB annotation. |
|
custom_pathway()
|
custom_pathway
Enables creation of a custom pathway binary matrix from a binmat() `object` |
|
dat.oncoPrint()
|
dat.oncoPrint
Enables creation of a matrix used to generate an OncoPrint heatmap. |
|
facets.dat()
|
facets.dat |
|
facets.heatmap()
|
facets.heatmap |
|
fusion
|
An example of fusions calls file from IMPACT cbioPortal dataset |
|
g.impact
|
List of curated genes for IMPACT |
|
gen.summary()
|
gen.summary |
|
get_tmb()
|
get_tmb
Function to calculate the tumor mutation burden of individual patients in a MAF file. Note that this can only be applied to
samples sequenced using one of the IMPACT panels. Other samples will be annotated as missing. |
|
ggcomut()
|
Co-mutation Heatmap of the Top Altered Genes |
|
gggenecor()
|
Correlation Heatmap of the Top Altered Genes |
|
ggheatmap()
|
Heatmap of all events after binmat |
|
ggsamplevar()
|
Histogram of Variants Per Sample Colored By Variant Classification |
|
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 palette |
|
gnomer_cols()
|
Function to extract colors from gnomer_colors as hex codes |
|
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 |
|
impact_genes
|
List of genes entrezID for the API |
|
maf_viz()
|
Creates a set of plot summarising a maf file. |
|
mut
|
An example maf file from IMPACT cbioPortal dataset |
|
oncokb()
|
OncoKB annotate |
|
plot_oncoPrint()
|
plot_oncoPrint
Creates the OncoPrint corresponding to the inputted genetic data |
|
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 |
|
substrRight()
|
Utility Function to Extract SNV |
|
tcga_genes
|
A vector of 19441 hugo symbols in TCGA |
|
tcga_samples
|
Data frame of all TCGA sample ids and their corresponding cancer type |
|
ti_341
|
Intervals sequenced in 341 panel |
|
ti_410
|
Intervals sequenced in 410 panel |
|
ti_468
|
Intervals sequenced in 468 panel |
|
uni.cox()
|
uni.cox
Performs univariate cox proportional hazard model on every feature |