getVariantScore: getVariantScore

In CNVfilteR: Identifies false positives of CNV calling tools by using SNV calls

Description

Returns score for a given allele frequency

Usage

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.