getVariantScore: getVariantScore

Description Usage Arguments Details Value

View source: R/getVariantScore.R

Description

Returns score for a given allele frequency

Usage

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getVariantScore(
  freq,
  expected.ht.mean,
  expected.dup.ht.mean1,
  expected.dup.ht.mean2,
  sigmoid.c1,
  sigmoid.c2.vector,
  sigmoid.int1,
  sigmoid.int2
)

Arguments

freq

Variant allele frequency

expected.ht.mean

Expected heterozygous SNV/indel allele frequency

expected.dup.ht.mean1

Expected heterozygous SNV/indel allele frequency when the variant IS NOT in the same allele than the CNV duplication call

expected.dup.ht.mean2

Expected heterozygous SNV/indel allele frequency when the variant IS in the same allele than the CNV duplication call

sigmoid.c1

Sigmoid c1 parameter

sigmoid.c2.vector

Vector containing sigmoid c2 parameters for the six sigmoids functions

sigmoid.int1

Sigmoid int 1

sigmoid.int2

Sigmoid int 2

Details

Returns a value between -1 and 1. If the allele frequency increases the evidence of discarding a CNV, then the score is positive. If the allele frequency decreases the evidence for discarding a CNV, the score is negative.

The model is based on the fuzzy logic and the score is calculated using sigmoids. See the vignette to get more details.

Value

variant score in the [-1, 1] range


CNVfilteR documentation built on April 17, 2021, 6:06 p.m.