Add dNdScv and expected mutated genomes to dev #217
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- pull covariates file at the beginning and pass it through missing: - still using global ref. transcripts
missing: - fix Rscript to store RefCDS also for non-mutated genes - clean inputs and outputs to keep only the custom RefCDS object and the covariates
…extract gene strand for the expected mutation R script
- add output to createpanels subworkflow - provide new input to expected mutrate and use it - remove filtering of three genes for bladder
Addittional amend to the commit: Change output files for simplicity
… into fix-non-mutated-rda
additional updates in steps to provide the right inputs pending: - fix in samples' sex metadata - still uncomplete RefCDS
- new parameter for the mutrisk_deepcsa script - auto turn on or off based on last input pending: -final testing in non-bladder project -fix pulling of file at the beginning or mounting file system -make decision on whether sample definition for expmutrate and for creating groups are independent or not -fix script when no mutations of gene-impact
- tmp fix: use global RefCDS object - remove dependency from expmutrate - check dndsout tables before writing avoid errors
6 tasks
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Adding dNdScv and expected mutated genomes to dev branch.
Still some details to fix related to running dNdScv with a custom definition of the reference transcripts but for now it can be run using the entire genes as a reference.
See #215 for a more detailed description.