How to extend MSPC package ? Here is what came to my mind !!

MSPC package primal

First attempt of developing MSPC package is aim to implement algorithm that proposed by paper called "combine evidence of chip-seq peak for multiple replicates". MSPC package can does following:

1. evaluate user given peak as stringent or weak peak by looking at its p value

2. further evaluate the analysis result of step one, regarding peaks, report overlapped peak from other Replicate

3. Based on the results of step 2, peak can be evaluated by Fisher test, and report its combine evidence of the peak; WHERE result could be generated as stringent_confirmed or weak confirmed if peak were stringent in step 1, or stringent discarded or weak discarded if peak were are weak in step 1.

4. if peak can pass Fisher test, also can carry on BH correction test to the peaks and adjust pvalue instead

MSPC package Extention

if MSPC package primal can be done in well manner and able to deliver to Bioconductor repository. Then think about extra feature of the package. This is my initial idea how to extend MSPC package' features:

1. data visualization: plot the peak (stringent peak, weak peak, stringent_confirmed, weak_discarded, and so on); visualize the peak.

2. Or develop handy web shinyapp (a.k.a, is handy web oriented data products), the main purpose to ease burden some of using MSPC package only in R environment, allow user to analyze their own peak data by accessing web such as Galaxy genome analyzer or bed tools did. Try to think about this and how is the feasibility of doing shinyapp and potential usage.

3. Or something else can bolster or enrich feature of MSPC package at the end.