Table 1.

Summary of four sex prediction tools for DNA methylation samples

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