ad.correct: Correct allele depth values

In rCNV: Detect Copy Number Variants from SNPs Data

Correct allele depth values

Description

A function to correct depth values with odd number of coverage values due to sequencing anomalies or miss classification where genotype is homozygous and depth values indicate heterozygosity. The function adds a value of one to the allele with the lowest depth value for when odd number anomalies or make the depth value zero for when miss-classified. The genotype table must be provided for the latter.

Usage

ad.correct(
  het.table,
  gt.table = NULL,
  odd.correct = TRUE,
  verbose = TRUE,
  parallel = FALSE
)

Arguments

het.table	allele depth table generated from the function hetTgen
gt.table	genotype table generated from the function hetTgen
odd.correct	logical, to correct for odd number anomalies in AD values. default TRUE
verbose	logical. show progress. Default TRUE
parallel	logical. whether to parallelize the process

Value

Returns the coverage corrected allele depth table similar to the output of hetTgen

Author(s)

Piyal Karunarathne

Examples

## Not run: adc<-ad.correct(ADtable)

rCNV documentation built on Sept. 30, 2024, 9:39 a.m.