README.md

In julaiti/MSPC: Multiple Sample Peak Calling: Using combined evidence from replicates to evaluate ChIP-seq peaks

MSPC : Bioconductor Package for Multiple Sample Peak Calling

MSPC packages implements set of functions to retrieve overlapped enriched regions across multiple replicates in parallel (a.k.a, pair-wise), statistical method for overlapped regions. simultaneous presence of an enriched regions in replicates experiment would justify a local decrease of the stringency criterion, leveraging on the principal that repeated evidence is compensating for weak evidence. This packages jointly analyzes the enriched regions of multiple replicates, distinguishing between biological and technical replicates, and accepting user defined parameters. Goal of developing R/Bioconductor package of Multiple Sample Peak Calling, to implement our algorithm in R and make sure R community get benefit from our method to solve issue raised by high-throughput genomic data.

Original method is presented in [@Vahid_Jalili_MSPC_2015]. Vahid Jalili, Matteo Matteucci, Marco Masseroli,and Marco J. Morelli : Using combined evidence from replicates to evaluate ChIP-seq peaks. Bioinformatics 2015, 31(17):2761-2769.doi:[10.1093/bioinformatics/btv293] (http://bioinformatics.oxfordjournals.org/content/31/17/2761.full). MSPC method was implemented in C# programming language and publicly available at https://mspc.codeplex.com. Graphical version of MSPC software can be found and available at project site http://musera.codeplex.com.

MSPC Package dependencies

Depends:
    R(>= 3.6)
Imports:
    GenomicRanges,
    rtracklayer,
    S4Vectors,
    IRanges,
    dplyr,
    magrittr,
    purrr,
    tidyr,
    ggplot2

Local files:

    MSPC_Package.R
    readPeakFile.R
    denoise_ER.R
    exportER.R
    getPlot.R
    runMSPC.R
    FDR_stats.R
    utilities.R
    zzz.R

MSPC implementation pipeline

Here is final stage of full-stack implementation of MSPC package:

Result of Enrichment Analysis

MSPC package has been tested with Myc TF public datasets in K562 human cells available from ENCODE project, result was validated with verified software tool MuSERA1 under same parameter setting, whereas accuracy reaches 96%.

Also MSPC package provides benchmark result for testing different number of input replicate sample down below:

julaiti/MSPC documentation built on Oct. 17, 2019, 9:44 p.m.