MethTargetedNGS (version 1.4.0)

compare_samples: Complete Methylation Analysis of Next Generation Sequencing Data

Description

This function perform complete methylation analysis of the data.

1. Visualize methylation pattern

2. Calculate methylation average

3. Calculate methylation entropy

4. Perform fisher exact test on the samples to identify significant CpG sites.

Usage

compare_samples(healthy, tumor)

Arguments

healthy

: Output Matrix from methAlign

tumor

: Output Matrix from methAlign

Value

Generate a plot of Methylation Average, Methylation Entropy, Fisher Exact Test and Log Odd Ratio

See Also

methAlign, methAvg, methEntropy, odd_ratio, fishertest_cpg,

Examples

healthy = system.file("extdata", "Healthy.fasta", package = "MethTargetedNGS")
tumor = system.file("extdata", "Tumor.fasta", package = "MethTargetedNGS")
reference =  system.file("extdata", "Reference.fasta", package = "MethTargetedNGS")

healthy = methAlign(healthy,reference)
tumor = methAlign(tumor,reference)
compare_samples(healthy,tumor)