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Huising-Lab / epiRomics

An R package designed to integrate and visualize various levels of epigenomic information, including but not limited to: ChIP, Histone, ATAC, and RNA sequencing. epiRomics is also designed to identify enhancer and enhanceosome regions from these data.

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Create sub-function to identify RNA expressed transcript as opposed to full gene model

ammawla opened this issue · comments

commented

Create sub-function to identify RNA expressed transcript as opposed to full gene model. Without this, issues in visualization arise for certain genes that have a very large gene model, but a smaller transcript model that is actually expressed.

commented

Counts data by transcript could be utilized, but would need to use ensembl id. Could write another sub function to check transcript id and convert, if necessary. But, may not be most pragmatic if user has bigwigs but no counts, or counts summarized by gene as opposed to transcript.

Other option is bigwig signal average summary per transcript within gene model, and decision making then. Foresee conflict if multiple transcripts of significantly varying size/length have close enough coverage.