getPurity {InfiniumPurify}

Estimate the tumor purity for 450K methylation data

Description

Estimate the percentage of tumor cells in cancer samples which are mixtures of cancer and normal cells.added a sentence

Usage

getPurity(tumor.data,normal.data = NULL,tumor.type = NULL)

Arguments

tumor.data

numeric vector/matrix of beta values for tumor samlpes. The names/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.

tumor.type

cancer type (in abbreviation) of tumor and normal samlpes. Options are "LUAD", "BRCA" and so on. See CancerTypeAbbr for detail.

Details

Arguments normal.data and tumor.type could be null. If either the number of tumor samples or number of normal smaples is less than 20, the tumor.type argument should be specified according to CancerTypeAbbr. If the numbers of tumor and normal samples are both more than 20, tumor.type could be null. In such case, getPurity first identify 1000 iDMCs by Wilcox rank-sum test, then tumor purity for each sample is estimated as the density mode of adjusted methylation levels of iDMCs.

Value

A vector of tumor purities for each tumor sample.

Author(s)

Xiaoqi Zheng [e-mail].

References

N. Zhang, H.J. Wu, W. Zhang, J. Wang, H. Wu and X. Zheng (2015) Predicting tumor purity from methylation microarray data. Bioinformatics 31(21), 3401-3405.

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, accepted.

Examples

## load example data
data(beta.emp)

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

## call purity for single tumor sample 
purity <- getPurity(tumor.data = tumor.data[,1],normal.data = NULL,tumor.type= "LUAD")

## call purity for less than 20 tumor samples
purity <- getPurity(tumor.data = tumor.data[,1:10],normal.data = NULL,tumor.type= "LUAD")

## call purity for more than 20 tumor samples with matched normal samples
purity <- getPurity(tumor.data = tumor.data[,1:40],normal.data = normal.data)