Calculates the original coverage for a segment based on its segment mean (log2 ratio), gender, chromosome, and assumed diploid coverage.
Usage
SegmentMeanToOriCov(SM, gender, chromosome, diploid_cov)
Arguments
- SM
Numeric. The segment mean (log2 ratio) from CNV analysis.
- gender
Character. Sample gender, either "male" or "female".
- chromosome
Character or factor. Chromosome name (e.g., "1", "2", ..., "X", "Y").
- diploid_cov
Numeric. The expected coverage for a diploid region (e.g., 100).
Value
Numeric. The estimated original coverage for the segment.
Details
For males and sex chromosomes ("X" or "Y"), the diploid coverage is halved.
For all other cases, the segment mean is scaled by the full diploid coverage.
Examples
SegmentMeanToOriCov(SM = 0, gender = "male", chromosome = "X", diploid_cov = 100)
#> [1] 50
SegmentMeanToOriCov(SM = 0.5, gender = "female", chromosome = "3", diploid_cov = 100)
#> [1] 141.4214
