estimateM: Estimate methylation M-value matrix
In methylumi: Handle Illumina methylation data

Description Usage Arguments Details Value Author(s) References

Estimate methylation M-value matrix from MethyLumiM-class object or eSet-class object, which include methylated and unmethylated probe intensities

1	estimateM(methyLumiM, returnType=c("ExpressionSet", "matrix"), offset=100)

`methyLumiM`	MethyLumiM-class object or eSet-class object, which include methylated and unmethylated probe intensities
`returnType`	determine whether return an ExpressionSet (MethyLumiM in this case) or matrix object
`offset`	offset added to the methylated and unmethylated probe intensities when estimating the M-value

M-value is the log2 ratio between Illumina methylated and unmethylated probe intensities. As variations of small intensities can cause big changes in the ratio estimation, so an offset is added to methylated and unmethylated probe intensities when estimating the M-value.

Please check the lumi package for more details of estimateM function.

A MethyLumiM or matrix object of methylation M-value

Pan DU

Du, P., Zhang, X, Huang, C.C., Jafari, N., Kibbe, W.A., Hou, L., and Lin, S.M., (2010) 'Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis', (under review)

methylumi documentation built on Nov. 8, 2020, 6:26 p.m.