Table 1 Summary of four sex prediction tools for DNA methylation samples
From: DNA methylation-based sex classifier to predict sex and identify sex chromosome aneuploidy
Package | Function name | Input requirements | Mechanism | Performance on clustering females and males | SCA detection |
|---|---|---|---|---|---|
Minfi | getSex | IDATs | Compare the log2 transformed median total intensity of probes mapped on ChrX and ChrY. | Good in clustering males and less well in clustering females | Not provided |
Ewastools | check_sex | IDATs | Compare the normalized average signal intensity of probes mapped on sex chromosomes | Excellent in clustering males and good in clustering females | Not provided |
sEst | estimateSex | Beta values and detection p-values | Group beta values and detection p-values into defined intervals and PCAs on the distribution patterns of these intervals. | Excellent in clustering males and females | Proposed but not validated |
WaterRmelon | estimateSex | Beta values (which can be easily generated from signal intensity text files or IDATs) | PCAs on beta values of sex differently methylated CpGs on ChrX and ChrY separately. | Excellent in clustering males and females | Proposed and validated by five Turner syndrome cases and one Klinefelter syndrome case |