In chedonat/OncoPhase: SOMATIC MUTATION CELLULAR PREVALENCE COMPUTATION

This is a generic function computing the cellular prevalence of somatic mutations in cancer using haplotype phasing. The model compute the prevalence of a somatic mutation relatively to close and phased germline mutation. It uses three sources of information as input : The allelic counts, the phasing information and the copy number alteration.

Vignette Info

getPrevalence(snp_allelecount_df, ref_allelecount_df, phasing_association_df, major_copynumber_df, minor_copynumber_df, normalfraction_df, nbFirstColumns = 3, method = "oxford1", tumoursamples = NULL, region = NULL)

Styles

snp_allelecount_df
A data frame containing for each mutation the allelic count of the variant at each tumour. Should contains at least Chrom (The mutation chromosome) , End (The mutation position) and IsGermline (is the mutation a Germline or Somatic) among the first columnns. ref_allelecount_df
A data frame containing for each mutation the allelic count of the reference at each tumour.Should contains at least Chrom (The mutation chromosome) , End (The mutation position) and IsGermline (is the mutation a Germline or Somatic) among the first columnns. phasing_association_df
A data frame containing for each somatic mutation, a colon separated list of germline SNP phased to it. major_copynumber_df A data frame containing for each mutation the major chromosonal copy number at each tumour sample. minor_copynumber_df A data frame containing for each mutation the minor chromosonal copy number at each tumour sample. normalfraction_df
A data frame containing for each mutation the fraction of normal cell contamination at each tumour/sample of the study. nbFirstColumns
Number of first columns in snp_allelecount_df to reproduce in the output dataframe e.g: Chrom, Pos, Vartype. method
The method to be used (default : oxford1 , alternatives are oxford2 , oxford3.) tumoursamples
The list of tumour samples to consider for the prevalence computation. This samples should be present as column header in the data frames snp_allelecount_df, ref_allelecount_df, major_copynumber_df,minor_copynumber_df and normalfraction_df. If not provided, the headers from nbFirstColumns + 1 to the last column of snp_allelecount_df is retrieved and its intersection with the headers of the four othe rmatrices is considered as the tumour samples of the allelecount or copy number matrices) Region
The region of the genome to consider in the format chrom:start-end e.g "chr22:179800-98767