GRaNIE issueshttps://git.embl.de/grp-zaugg/GRaNIE/-/issues2021-02-04T19:36:36Zhttps://git.embl.de/grp-zaugg/GRaNIE/-/issues/10Add SNP-peak links2021-02-04T19:36:36ZJudith ZauggAdd SNP-peak linksIn addition to the TF-peak links that we have it would be useful to also have SNP - peak links in the network.
* possible implementation: generate list of relevant SNP-peak annotations outside of pipeline, then provide this additional i...In addition to the TF-peak links that we have it would be useful to also have SNP - peak links in the network.
* possible implementation: generate list of relevant SNP-peak annotations outside of pipeline, then provide this additional information to the function that constructs the GRN
This will allow to also keep links in the network that are not necessarily regulated by a TF across the individuals, but by a genetic variant associated to the peak.Additional functions and methodsChristian ArnoldChristian Arnoldhttps://git.embl.de/grp-zaugg/GRaNIE/-/issues/9SNP integration: Feature and implementation details2021-02-04T19:36:40ZChristian ArnoldSNP integration: Feature and implementation detailsImplemented due to Neha's suggestion, test feature and whether is functions flexibly enough.
Current implementation:
1. Input: list of SNP positions and SNP genome assembly (rsid not enough) and GRN
2. Overlap peaks with SNP positions a...Implemented due to Neha's suggestion, test feature and whether is functions flexibly enough.
Current implementation:
1. Input: list of SNP positions and SNP genome assembly (rsid not enough) and GRN
2. Overlap peaks with SNP positions and add (1) number of overlapping SNPs and (2) SNP annotation for each peak
3. The returned modified GRN data frame then contains additional columns that can be used for filtering etc
Would it also be helpful to do the same with genes?Additional functions and methodsNeha DagaNeha Daga