inferSex: Infer Sex

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Description

Infer Sex

Usage

inferSex(sset)

Arguments

sset

a SigSet

Value

'F' or 'M' We established our sex calling based on the median intensity of chromosome X, Y and the fraction of intermediately methylated probes among the identified X-linked probes. This is similar to the approach by Minfi (Aryee et al., 2014) but also different in that we used the fraction of intermediate beta value rather than median intensity for all chromosome X probes. Instead of using all probes from the sex chromosomes, we used our curated set of Y chromosome probes and X-linked probes which exclude potential cross-hybridization and pseudo-autosomal effect.

XXY male (Klinefelter's), 45,X female (Turner's) can confuse the model sometimes. Our function works on a single sample.

Examples

sset <- sesameDataGet('EPIC.1.LNCaP')$sset
inferSex(sset)

sesame documentation built on Nov. 15, 2020, 2:08 a.m.