QSEA package - Enrichement parameters choice (addEnrichmentParameters)

Question

[lech.kaczmarczyk]

Hi All, I am using QSEA to analyze MeDIP data. I am stuck on the step where enrichment parameters need to be defined (FUN addEnrichmentParameters). To get the rough idea about the data, I input the defaults. But now I would like to make sure they are the right choice. To quote the help of the FUN:

**enrichmentPattern**   
The name of the pattern, on which the enrichment depends on (usually CpG for methylation analysis). This name must correspond to the name specified in addPatternDensity()
**windowIdx**   
vector of window indices, for which "true" values are known (or can be estimated)
**signal**  
Matrix containing the known (or estimated) values for all samples and all specified windows, as a numeric matrix. These values are expected to be between 0 and 1.
**bins**    
For the enrichment analysis, windows are binned according to pattern density. This parameter specifies the bins.
**min_wd**  
minimal number of windows per bin to be considered

Could someone please enlighten me on the meaning of those parameters, and how to choose the optimal ones to get most reliable data? The vignette warns that improper parameters may lead to false result. Obviously I would like to avoid the latter. My samples are from mammalian tissue, I don't have the inputs (prior to MeDIP). No cancer tissue. It's my first time with MeDIP.

Thanks in advance for educating me.

Cheers, Lech

[venu]

It is described in the tutorial here (Section: 3.2.3)

[lech.kaczmarczyk]

Thanks for that. Yes, I read that, but found it somehow not exhausting the topic. Sorry for my lack of understanding.