gv_mut_signatures: gv_mut_signatures

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_signatures

Description

Predicts the contribution of known mutational processes to the samples.

Usage

gv_mut_signatures(
  muts,
  metadata,
  response,
  gbuild = "BSgenome.Hsapiens.UCSC.hg19",
  mut_sigs = "COSMIC_v2_SBS_GRCh37",
  tri.counts.method = "default",
  colors = c("black", "orange"),
  col.names = TRUE
)

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.
gbuild	Version of the genome to work with. It can be one of the following: - ‘BSgenome.Hsapiens.UCSC.hg19’ - ‘BSgenome.Hsapiens.UCSC.hg38’ - ‘BSgenome.Mmusculus.UCSC.mm10’ - ‘BSgenome.Mmusculus.UCSC.mm39’
mut_sigs	Mutational signature matrices containing the frequencies of all nucleotide changes per signature need to be indicated. GEGVIC contains the matrices from COSMIC for single and double base substitutions. To choose one, the user has to indicate ’COSMIC_vXX_YYBS_GRChZZ’ in the mut_sigs argument. The XX is the version, that can be v2 or v3.2. YY indicates if mutations are single (S) or double (D) base substitutions, while the ZZ is for the genome assembly, either GRCh37 or GRCh38 for human data and mm9 or mm10 for mouse data.
tri.counts.method	Normalization method. Needs to be set to either: - 'default' – no further normalization. - 'exome' – normalized by number of times each trinucleotide context is observed in the exome. - 'genome' – normalized by number of times each trinucleotide context is observed in the genome. - 'exome2genome' – multiplied by a ratio of that trinucleotide's occurence in the genome to the trinucleotide's occurence in the exome. - 'genome2exome' – multiplied by a ratio of that trinucleotide's occurence in the exome to the trinucleotide's occurence in the genome. - data frame containing user defined scaling factor – count data for each trinucleotide context is multiplied by the corresponding value given in the data frame.
colors	Character vector indicating the colors of the different groups to compare. Default values are two: black and orange.
col.names	Logical value to determine if tumour are shown in plots.

Value

Returns ggplot objects and the results table in a form of a data frame.

Examples

mut.sigs <- gv_mut_signatures(muts = sample_mutations,
                              metadata = sample_metadata,
                              response = MSI_status,
                              gbuild = 'BSgenome.Hsapiens.UCSC.hg38',
                              mut_sigs = 'COSMIC_v2_SBS_GRCh38',
                              tri.counts.method = 'default',
                              colors = c('orange', 'black'),
                              col.names = TRUE)

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