check_fit: Sample QC

In mskcc/facets-suite: Functions to run and parse output from FACETS

Sample QC

Description

Generate QC metrics for sample. Can use mutation calls in MAF file.

Usage

check_fit(facets_output, genome = c("hg19", "hg18", "hg38"),
  algorithm = c("em", "cncf"), maf = NULL)

Arguments

facets_output	Output from run_facets.
genome	Genome build.
algorithm	Choose assessing the fit from the em or cncf algorithm.
maf	Optional: mutation calls for assessed samples, should only include mutations for given sample.

Value

A list object with the following items:

• diplogr_flag: Boolean indicating extreme dipLogR value.

• n_alternative_diplogr: Number of alternative dipLogR values.

• n_dip_bal_segs, frac_dip_bal_segs: Number of balanced segments at dipLogR and the fraction of genome they represent.

• n_dip_imbal_segs, frac_dip_imbal_segs: Number of imbalanced segments at dipLogR and the fraction of genome they represent.

• n_amp: Number of segments at total copy number >= 10.

• n_homdels: Number of homozygously deleted segments (total copy number = 0).

• n_homdels_clonal, frac_homdels_clonal: Number of clonal homdel segments and the fraction of the genome they represent.

• n_cn_states: Number of unique copy-number states (i.e. combinations of major and minor copy number).

• n_segs: Number of segments.

• n_cnlr_clusters: Number of copy-number log-ratio clusters

• n_lcn_na: Number of segments where no minor copy number was inferred (lcn is NA).

• n_loh, n_loh: Number of segments where the minor copy number is 0 and the fraction of the genome they represent.

• n_snps: Number of SNPs used for segmentation.

• n_het_snps, frac_het_snps: Number of heterozyous SNPs used for segmentation and their fraction of the total.

• n_het_snps_hom_in_tumor_1pct, frac_het_snps_hom_in_tumor_1pct: Number of heterozyous SNPs where the tumor allele frequency is <0.01/>0.99 their fraction of the total.

• n_het_snps_hom_in_tumor_5pct, frac_het_snps_hom_in_tumor_5pct: Number of heterozyous SNPs where the tumor allele frequency is <0.05/>0.95 their fraction of the total.

• mean_cnlr_residual, sd_cnlr_residual: Mean and standard deviation of SNPs' log-ratio from their segments copy-number log-ratio.

• n_segs_discordant_tcn, frac_segs_discordant_tcn: Number of segments where the naïve and EM algorithm estimates of the total copy number are discordant and the fraction of the genome they represent.

• n_segs_discordant_lcn, frac_segs_discordant_lcn: Number of segments where the naïve and EM algorithm estimates of the minor copy number are discordant and the fraction of the genome they represent.

• n_segs_discordant_both, frac_segs_discordant_both: Number of segments where the naïve and EM algorithm estimates of the both copy numbers are discordant and the fraction of the genome they represent.

• n_segs_icn_cnlor_discordant, frac_icn_cnlor_discordant: Number of clonal segments where the log-ratio shows balance but the copy-number solution does not, and the reverse, and the fraction of the genome they represent.

• dip_median_vaf: If MAF input: median tumor VAF of somatic mutations on clonal segments with total copy number 2 and allelic balance.

• n_homdel_muts: If MAF input: number of somatic mutations in homozygously deleted segments.

• median_vaf_homdel_muts: If MAF input: Median tumor VAF of somatic mutations homozygously deleted segments.

mskcc/facets-suite documentation built on Sept. 13, 2022, 4:14 a.m.