Assigns a quality tag ("PASS" or "FAILED") to a segment based on the maf GMM weight and probe count thresholds.
Usage
AddQualTag(Chromosome, MAF_gmm_weight, MAF_Probes, MAF_gmm_G, snpmin)
Arguments
- Chromosome
Character.
- MAF_gmm_weight
Numeric. The mixture weight of the most prominent maf GMM cluster.
- MAF_Probes
Integer. The number of nonzero maf probes in the segment.
- MAF_gmm_G
Integer. Number of maf GMM clusters.
- snpmin
Integer. The minimum nonzero SNP count.
Value
Character. "PASS" if the segment passes quality checks, "FAILED" otherwise.
Details
A segment is marked as "PASS" if the maf GMM weight is at least 0.35 and the probe count is at least twice the minimum SNP count (snpmin). Otherwise, it is marked as "FAILED".
Examples
AddQualTag(Chromosome = "1", MAF_gmm_weight = 0.4, MAF_Probes = 20, MAF_gmm_G = 2, snpmin = 7)
#> [1] "PASS"
AddQualTag(Chromosome = "X", MAF_gmm_weight = 0.2, MAF_Probes = 10, MAF_gmm_G = 1, snpmin = 7)
#> [1] "Exclude"
