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metevalue (version 0.2.4)

E-Value in the Omics Data Association Studies

Description

In the omics data association studies, it is common to conduct the p-value corrections to control the false significance. Beyond the P-value corrections, E-value is recently studied to facilitate multiple testing correction based on V. Vovk and R. Wang (2021) . This package provides E-value calculation for DNA methylation data and RNA-seq data. Currently, five data formats are supported: DNA methylation levels using DMR detection tools (BiSeq, DMRfinder, MethylKit, Metilene and other DNA methylation tools) and RNA-seq data. The relevant references are listed below: Katja Hebestreit and Hans-Ulrich Klein (2022) ; Altuna Akalin et.al (2012) .

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Version

Install

install.packages('metevalue')

Monthly Downloads

160

Version

0.2.4

License

Apache License (>= 2)

Maintainer

Yifan Yang

Last Published

May 26th, 2023

Functions in metevalue (0.2.4)

metevalue.DMRfinder

Calculate E-value of the DMRfinder data format

metevalue.DMRfinder.chk

Check the DMRfinder data format

metevalue.biseq.chk

Check the BiSeq data format

metevalue.methylKit

Calculate E-value of the methylKit data format

demo_methylkit_methyrate

Methyrate Dataset

metevalue.metilene.chk

Check the Metilene data format

metevalue.metilene

Calculate E-value of the Metilene data format

metevalue.methylKit.chk

Check the methylKit data format

metevalue.biseq

Calculate E-value of the BiSeq data format

metevalue.RNA_general

A general method to calculate the e-value for RNA-seq data.

evalue_buildin_var_fmt_nm

Build-in check file format function Perform the format check and data clean for the "metilene" or "biseq", "DMRfinder" or "methylKit" method correspondingly.

demo_metilene_out

Metilene Demo Output Dataset

varevalue.metilene

Calculate E-value of the Metilene data

varevalue.single_general

A general method to calculate the e-value for other DNA methylation tools not described above. The input data is the DNA methylation rates using the similar format with Metilene.

demo_metilene_input

Metilene Methyrate Demo Dataset

evalue_buildin_sql

Build-in data process function

demo_biseq_methyrate

BiSeq Methyrate Demo Dataset

demo_DMRfinder_rate_combine

DMRfinder Methyrate Demo Dataset

demo_methylkit_met_all

Methyrate output dataset from methylKit

demo_DMRfinder_DMRs

DMRfinder Output Demo Dataset

DESeq Output Dataset

BiSeq Output Demo Dataset