f_test: Find differentially methylated CpGs of interest between...

In kevinlul/EpigeneLite: Lite version of EpigenCentral

Description

Find differentially methylated CpGs of interest between designated cases and controls. We use minfi's dmpFinder, which performs an F-test, and then we further filter for significance thresholds p < 0.05 and delta beta > 0.1.

Usage

f_test(grset)

Arguments

grset

minfi GenomicRatioSet containing beta values

Value

data frame containing differentially methylated CpGs of interest, annotated with their genomic location, sorted by fdr adjusted p-value and delta beta, with mean values at this position for reference

References

Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA (2014). “Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays.” Bioinformatics, 30(10), 1363-1369. doi: 10.1093/bioinformatics/btu049 (URL: https://doi.org/10.1093/bioinformatics/btu049).

Examples

## Not run: 
grset <- read_idat("extdata/GSE55491/samplesheet.rss-GSE55491.csv")
pca_plot(grset)

## End(Not run)

kevinlul/EpigeneLite documentation built on Dec. 21, 2021, 6:35 a.m.