methylMnM: detect different methylation level (DMR)

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

Author
Yan Zhou, Bo Zhang, Nan Lin, BaoXue Zhang and Ting Wang
Date of publication
None
Maintainer
Yan Zhou<zhouy1016@163.com>
License
GPL-3
Version
1.12.0

View on Bioconductor

Man pages

calcFactornew
Normalization factor.
calculatecount
Call C programs to R.
calculatecount1
Call C programs to R.
calculatecountneg
Call C programs to R.
CNVnormal
Normalize copy number variation (CNV).
countcpgbin
Compute the total CpG number of each bin with each CpG site.
countMeDIPbin
Compute the total MeDIP-seq number of each bin.
countMREbin
Compute the total MRE-seq number of each bin.
countMREcpgbin
Compute the MRE CpG number of each bin with MRE CpG sites.
cpgcount
Call C programs to R.
MnM-package
MeDIP-Seq and MRE-Seq data analysis
MnM.qvalue
Estimate the q-values for a given set of p-values
MnM.selectDMR
Select significants of each comparation.
MnM.test
Compute p-value of each bin.
normpdf
Compute p-value with normal distribution.
normpdf1
Compute p-value with normal distribution.
pmultinom
Call C programs to R.
qvalue.rank
Rank values.
removeblacklist
Remove blacklist.

Files in this package

methylMnM/DESCRIPTION
methylMnM/NAMESPACE
methylMnM/R
methylMnM/R/CNVnormal.R
methylMnM/R/MnM.qvalue.R
methylMnM/R/MnM.selectDMR.R
methylMnM/R/MnM.test.R
methylMnM/R/calcFactornew.R
methylMnM/R/calculatecount.R
methylMnM/R/calculatecount1.R
methylMnM/R/calculatecountneg.R
methylMnM/R/countMREbin.R
methylMnM/R/countMREcpgbin.R
methylMnM/R/countMeDIPbin.R
methylMnM/R/countcpgbin.R
methylMnM/R/cpgcount.R
methylMnM/R/normpdf.R
methylMnM/R/normpdft1.R
methylMnM/R/pmultinom.R
methylMnM/R/qvalue.rank.R
methylMnM/R/removeblacklist.R
methylMnM/build
methylMnM/build/vignette.rds
methylMnM/inst
methylMnM/inst/doc
methylMnM/inst/doc/methylMnM.R
methylMnM/inst/doc/methylMnM.Rnw
methylMnM/inst/doc/methylMnM.pdf
methylMnM/inst/extdata
methylMnM/inst/extdata/H1ESB1_MRE_18.extended.txt
methylMnM/inst/extdata/H1ESB1_MeDIP_18.extended.txt
methylMnM/inst/extdata/H1ESB2_MRE_18.extended.txt
methylMnM/inst/extdata/H1ESB2_Medip_18.extended.txt
methylMnM/inst/extdata/all_CpGsite_chr18.txt
methylMnM/inst/extdata/three_Mre_CpGsite_chr18.txt
methylMnM/man
methylMnM/man/CNVnormal.Rd
methylMnM/man/MnM-package.Rd
methylMnM/man/MnM.qvalue.Rd
methylMnM/man/MnM.selectDMR.Rd
methylMnM/man/MnM.test.Rd
methylMnM/man/calcFactornew.Rd
methylMnM/man/calculatecount.Rd
methylMnM/man/calculatecount1.Rd
methylMnM/man/calculatecountneg.Rd
methylMnM/man/countMREbin.Rd
methylMnM/man/countMREcpgbin.Rd
methylMnM/man/countMeDIPbin.Rd
methylMnM/man/countcpgbin.Rd
methylMnM/man/cpgcount.Rd
methylMnM/man/normpdf.Rd
methylMnM/man/normpdf1.Rd
methylMnM/man/pmultinom.Rd
methylMnM/man/qvalue.rank.Rd
methylMnM/man/removeblacklist.Rd
methylMnM/src
methylMnM/src/CpGcount.c
methylMnM/src/calculatecount.c
methylMnM/src/calculatecount1.c
methylMnM/src/calculatecountneg.c
methylMnM/src/methylmnm.h
methylMnM/src/pmultinom.c
methylMnM/src/pvalueclassify.c
methylMnM/src/register.c
methylMnM/vignettes
methylMnM/vignettes/methylMnM.Rnw