InfiniumPurify (version 1.3.1)

InfiniumDMC: Differentially Methylation Calling accounting for tumor purity

Description

Infer differentially methylated CpG sites with the consideration of tumor purities.

Usage

InfiniumDMC(tumor.data,normal.data,purity,threshold)

Arguments

tumor.data

numeric matrix of beta values for tumor samlpes. The rownames of tumor.data should be probe names of Infinium 450k array, and colnames should be names of tumor samples.

normal.data

numeric matrix of beta values for normal samlpes. The rownames of normal.data should be probe names of Infinium 450k array, and colnames should be names of normal samples.

purity

purities for tumor samples. Could be estimated by getPurity, or user specified purities from other tools.

threshold

probability threshold in control-free DM calling. Default is 0.1.

Value

A data frame of statistics, p-values and q-values for all CpG sites.

Details

If normal.data is provided, the function tests each CpG site for differential methylation between tumor and normal samples with the consideration of tumor purities by a generalized linear regression. If normal.data is not provided, the function computes posterior probability to rank CpG sites.

References

X. Zheng, N. Zhang, H.J. Wu and H. Wu, Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies. Genome biology, in revision.

See Also

dmpFinder in the minfi package.

Examples

## load example data
data(beta.emp)

normal.data <- beta.emp[,1:21]
tumor.data <- beta.emp[,22:61]

## estimate tumor purity
purity <- getPurity(tumor.data = tumor.data,normal.data = normal.data)

## DM calling with normal controls
DMC = InfiniumDMC(tumor.data = tumor.data,normal.data = normal.data,purity = purity)

## DM calling without normal control
DMC_ctlFree = InfiniumDMC(tumor.data = tumor.data,purity = purity)