generate_all_models: Generate All Models

In andygxzeng/ECSI: Espresso - Somatic Mutation Calling using Contextual Error Models

Description

Generate all error models for each trinucleotide variant context. Fits error distribution with either an Exp or Weibull distribution depending on the overall distribution of non-reference alleles. If the most frequent non-reference allele count is 1 (typically at <10,000 sequencing depth) an Exponential distribution will be fitted and if it is greater than 1 (seen at ultra-deep read depths) a Weibull distribution will be fitted.

Usage

generate_all_models(sample, model = "auto")

Arguments

sample	VRanges object of the varscan pileup2cns output annotated with variant context
model	Specifying which error model ("exp" or "weibull") to fit. Default is "auto".

Value

This function returns a dataframe with the following information:

• FlankingSeqGroup

• Model Used (Exp or Weibull)

• Model parameter 1

• Model parameter 2

Examples

## Not run: 

# Get flagged alleles and cosmic mutations
heme_COSMIC <- load_cosmic_mutations(cosmic_mutations_path = "./heme_COSMIC.csv")
flagged_alleles <- get_flagged_alleles(all_samplele_names, all_samplele_paths,
    exclude_cosmic_mutations = TRUE, cosmic_mutations = heme_COSMIC, cosmic_mut_frequency = 3)

# Load and annotate samplele
sample <- load_as_VRanges(sample_name = "pt123",
    samplele_path = "./patient_123_pileup2cns", genome = "hg19", metadata = TRUE)
sample <- sequence_context(sample)
library(MafDb.gnomADex.r2.1.hs37d5)
annotated_sample <- annotate_MAF(varscan_output = variants,
    MAF_database = MafDb.gnomADex.r2.1.hs37d5, genome = "hg19")

# Filter model input
sample_model_input <- filter_model_input(model_input = annotated_sample,
    flagged_alleles = flagged_alleles, filter_cosmic_mutations = TRUE,
    cosmic_mutations = heme_COSMIC, cosmic_mut_frequency = 10)

# Generate the error models for this samplele
sample_models <- generate_all_models(sample = sample_model_input, plots = FALSE)


## End(Not run)

andygxzeng/ECSI documentation built on Feb. 6, 2021, 8:53 a.m.