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 |

**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.

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

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