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methylMnM (version 1.10.0)

detect different methylation level (DMR)

Description

To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparation.

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Version

Version

1.10.0

License

GPL-3

Maintainer

Yan Zhou

Last Published

February 15th, 2017

Functions in methylMnM (1.10.0)

CNVnormal

Normalize copy number variation (CNV).
MnM.test

Compute p-value of each bin.
removeblacklist

Remove blacklist.
calculatecount1

Call C programs to R.
methylMnM-package

MeDIP-Seq and MRE-Seq data analysis
calcFactornew

Normalization factor.
normpdf

Compute p-value with normal distribution.
qvalue.rank

Rank values.
normpdft1

Compute p-value with normal distribution.
pmultinom

Call C programs to R.
countMREbin

Compute the total MRE-seq number of each bin.
calculatecount

Call C programs to R.
countMREcpgbin

Compute the MRE CpG number of each bin with MRE CpG sites.
MnM.qvalue

Estimate the q-values for a given set of p-values
MnM.selectDMR

Select significants of each comparation.
countMeDIPbin

Compute the total MeDIP-seq number of each bin.
countcpgbin

Compute the total CpG number of each bin with each CpG site.
calculatecountneg

Call C programs to R.
cpgcount

Call C programs to R.