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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