Extract SNVs, CNVs and clones on genes of interest from superFreq output

Source: R/import_goi_superfreq.R

This function imports superFreq's SNVs, CNAs and clones for one patient and outputs them into a tidy format where every row is a variant.

import_goi_superfreq(superFreq_R_path = "", superFreq_meta_path = "",
  studyGenes = NULL, patientID = "D1", ref_genome = "hg38",
  min_vaf = 0.15, min_alt = 2, sev = 12)

Arguments

superFreq_R_path

Path to superFreq R folder.
superFreq_meta_path

Path to superFreq run cohort metadata saved in tab delimited file. See https://github.com/ChristofferFlensburg/superFreq for examples.
studyGenes

character vector containing genes of interest. If none provided all genes will be used.
patientID

a character vector specifying the patient/s id/s for which variants have to be imported.
ref_genome

character vector for the reference genome used in the analysis ('hg38' or 'hg19')
min_vaf

numeric. Minimum variant allele frequency (VAF) for a variant to be kept at one time point.
min_alt

numeric. Minimum number of reads supporting the alt allele at one time points for a patient.
sev

numeric. Only variants with severity value < sev are kept.

Value

a data frame that stores CNAs, SNVs and clones called by `superFreq` https://github.com/ChristofferFlensburg/superFreq on a set of `studyGenes` for `patientID`. CNAs, SNVs and clones are stored as explained in https://annaquaglieri16.github.io/varikondo/articles/how-variants-are-stored.html.