filter_data: Filtering DNA methylation 450k non_specific probes

In ABC.RAP: Array Based CpG Region Analysis Pipeline

Description

This function filters the reported nonspecific probes, and also filters probes that interrogate SNPs of minor allele frequency (MAF) > 0.1. A list of nonspecific probes was obtained from Chen et al (2013) supplementary files.

Usage

filter_data(x)

Arguments

x	The normalised beta values in a data matrix format, where conditions are arranged in columns and cg probes are arranged in rows.

References

Chen YA, Lemire M, Choufani S, et al. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics 2013;8:203-9.

Examples

data(test_data)
data(nonspecific_probes)
test_data_filtered <- filter_data(test_data)

ABC.RAP documentation built on May 2, 2019, 9:16 a.m.