fishertest_cpg: Perform Fisher Exact Test on Methylation Data.

Description Usage Arguments Value Author(s) See Also Examples

View source: R/sequenceAlignment.R

Description

Fisher exact test is a test to calculate the statistical significance using contingency table. It was used to find the statistically significant differences in the methylation status of one particular CpG site between healthy and tumor sample. Contingency matrix was created for each CpG site. P-value was corrected for multiple testing using Benjamini-Hochberg method to calculate False Discovery Rate (FDR)

Usage

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fishertest_cpg(healthy, tumor, plot = TRUE, main = "Fisher Exact Test")

Arguments

healthy

Matrix from methAlign. Also matrix where columns represents Cytosine of CpG sites and rows represents sequences.

tumor

Matrix from methAlign. Also matrix where columns represents Cytosine of CpG sites and rows represents sequences.

plot

Boolean. TRUE if need a plot after calculation. Default TRUE

main

Title of the plot. Default "Fisher Exact Test"

Value

Vector containing p-values.

Author(s)

Muhammad Ahmer Jamil, Prof. Holger Frohlich, Priv.-Doz. Dr. Osman El-Maarri

Maintainer: Muhammad Ahmer Jamil [email protected]

See Also

methAlign, compare_samples

Examples

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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)
fisherexacttest <- fishertest_cpg(healthy,tumor)

MethTargetedNGS documentation built on May 6, 2019, 2:04 a.m.