predictGA: Predict gestational age in days from conception

In JonBohlin/predictGA: Prediction of gestational age with Illumina HumanMethylation450 data

Description

The function predictGA takes a matrix with Illumina HumanMethylation450 type DNA methylation data. Column names must designate CpG sites (i.e. 'cgXXXXXX', X=number) and row names samples IDs.

Usage

predictGA(mldat, transp=TRUE, se=TRUE)

Arguments

mldat	A matrix containing DNA methylation beta values (0<=beta<=1)
transp	If TRUE (default), the transpose is automatically taken if the number of rows is greater than the number of columns.
se	If se=TRUE, the estimated coefficients are based on the prediction model with the lambda penalty term being allowed to vary up to one standard error within the minimum. If se=FALSE, the minimum lambda is assumed.

Details

The minimum lambda (se=FALSE) may result in slightly better predictions, however substantially more CpG sites are needed for estimation. Since the prediction difference is hardly noticeable se=TRUE is the default option.

Value

The function returns estimated gestational age predictions, together with samples IDs as row names, in a data.frame object.

Note

Requires quite a bit of memory due to the large DNA methylation matrix required for the prediction model.

Author(s)

Jon Bohlin

References

Jon Bohlin, Siri E. Haaberg, Per Magnus, et al. (2016). Prediction of gestational age based on genome-wide differentially methylated regions. Genome Biology (in review)

Jerome Friedman, Trevor Hastie, Robert Tibshirani (2010). Regularization Paths for Generalized Linear Models via Coordinate Descent. Journal of Statistical Software, 33(1), 1-22. URL http://www.jstatsoft.org/v33/i01/.

Examples

## Make a mock Illumina HumanMethylation450 type DNA methylation matrix
cpgs<-extractSites(type="se")
allcpgs<-extractSites(type="all")
numsamples<-100
mlmatr<-matrix(NA, ncol=length(allcpgs), nrow=numsamples)
mlmatr<-data.frame(mlmatr)
for(i in cpgs)
  mlmatr[,i]<-runif(numsamples, min=0, max=1)
## Perform gestational age prediction
mypred<-predictGA(mlmatr)

JonBohlin/predictGA documentation built on May 7, 2019, 12:03 p.m.