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sr320 / ceabigr

Workshop on genomic data integration with a emphasis on epigenetic data (FHL 2022)
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Create exon regression per gene #86

Closed kubu4 closed 4 months ago

kubu4 commented 7 months ago

Use this file to start:

https://github.com/sr320/ceabigr/blob/main/output/19-exon-expression/S12M-exon_expression.tab

sr320 commented 7 months ago

With this code https://github.com/sr320/ceabigr/blob/main/code/64-exon-expression.Rmd

was able to get... https://github.com/sr320/ceabigr/blob/main/output/64-exon-expression/exon-summary.csv

still needs some follow - through to understand... get p values

sr320 commented 7 months ago

quick look at data 000128

kubu4 commented 7 months ago

From Li et al. Sci. Adv. 2018;4:eaat2142:

Spurious transcription calcs:

Compute natural log fold change of expression relative to exon 1.

Higher levels of spurious transcription would result in higher ratios of expression for more distal exons.

This is due to their proposal that transcripts starting within the gene body would have increases in expression of more distal exons and less for more proximal exons.