gv_mut_summary: gv_mut_summary

In oriolarques/GEGVIC: A workflow to analyse Gene Expression, Genetic Variations and Immune cell Composition of tumour samples using Next Generation Sequencing data.

gv_mut_summary

Description

Given a table that contains genomic variants from samples of interest, it summarises different aspects of such mutations and draws an oncoplot.

Usage

gv_mut_summary(
  muts,
  metadata,
  response,
  top_genes = 10,
  specific_genes = NULL,
  col.names = TRUE,
  colors = c("black", "orange")
)

Arguments

muts	Data frame containing genomic variations. Necessary columns must have the following names: - Hugo_Symbol: Gene symbol from HGNC. - Chromosome: Affected chromosome. - Start_Position: Mutation start coordinate. - End_Position: Mutation end coordinate. - Reference_Allele: The plus strand reference allele at this position. Includes the deleted sequence for a deletion or "-" for an insertion. - Tumor_Seq_Allele2: Tumor sequencing discovery allele. - Variant_Classification: Translational effect of variant allele. Can be one of the following: Frame_Shift_Del, Frame_Shift_Ins, In_Frame_Del, In_Frame_Ins, Missense_Mutation, Nonsense_Mutation, Silent, Splice_Site, Translation_Start_Site, Nonstop_Mutation, RNA, Targeted_Region. - Variant_Type: Type of mutation. Can be: 'SNP' (Single nucleotide polymorphism), 'DNP' (Double nucleotide polymorphism), 'INS' (Insertion), 'DEL' (Deletion). - Tumor_Sample_Barcode: Sample name.
metadata	Data frame that contains supporting variables to the data.
response	Unquoted name of the variable indicating the groups to analyse.
top_genes	Number of genes to be analysed in the mutational summary.
specific_genes	Genes that will be plotted in the oncoplot.
col.names	Logical value to decide if tumour names are added to the plot.
colors	Character vector indicating the colors of the different groups to compare. Default values are two: black and orange.

Value

Prints two plots: A summary of sample mutations and an oncoplot.

Examples

gv_mut_summary(muts = sample_mutations,
               metadata = sample_metadata,
               response = MSI_status,
               top_genes = 10,
               specific_genes = NULL,
               col.names = TRUE,
               colors = c('orange', 'black'))

oriolarques/GEGVIC documentation built on Oct. 30, 2024, 10:44 p.m.