Added some extra data to the output of the analyzes such as the direction of the enrichment and a header. Also added classes that will be further used to centralize the analysis code. The EnrichmentDataReader class will be responsible for reading the data (for most analysis the read data will be returned as a GenomicBoundaries object). The eQtlDataParser reads and filters eQTL results on top and non top effects.
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Made changes to the EnrichmentDataReader and modified the tools such as SplitWigTextDataOnChromosome and WriteWigToText. Also added a histone enrichment test method to see what's wrong
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Made final changes to analysis code for the Transcription Factor Enrichment (fixed enrichment direction), added some more methods to the EnrichmentReader and HistoneSiteEnrichment. Added new class to perform Enrichment on output for regressing out results.
- tinkering with the violinboxplot (for smoother smoothing)
Merge molgenis/master
Minor edits
Merge pull request #186 from PatrickDeelen/master

Some improvements to file and exception handeling to metaQtl4
Merge molgenis/master
- adds dprime to conditional analysis
- Minor edit in TriTypertoPedAndMapConverter
Merge pull request #187 from harmjanwestra/master

Minor edits
Merge branch 'master' of https://github.com/molgenis/systemsgenetics
Last update on the code for now. I might want to clean my code later on (remove double code etc) I changed all enrichment analyses so that the entire genotype data is read and not a subset as not all permutations could be found.
Merge pull request #189 from PatrickDeelen/master

minor stuf
- Fix conditional analysis crashes when finding unexpected values in eQTL file.
- Code clean up of SNP filter
Merge pull request #188 from MatthieuBeukers/master

Last updates from me :)
Merge molgenis/master
Merge pull request #190 from harmjanwestra/master

Small fixes and code cleanup