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HYsxe / PRINT

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Loading back in chunked RDS data #9

Closed maxdudek closed 1 year ago

maxdudek commented 1 year ago

Hi,

After running getCountTensor() and getFootprints(), the results are (presumably) saved in chunkedCountTensor and chunkedFootprintResults. After restarting R, I now want to run getTFBS(), but I would prefer not to rerun the previous two commands since they take some time. How can I load the chunked rds data into my R project so I don't have to recalculate them? Couldn't find anything about it in the tutorial.

Thanks! Max

maxdudek commented 1 year ago

Oops, nevermind - I missed the bit of code that automatically loads in the rds if it already exists.

HYsxe commented 1 year ago

Glad you found it! In general getTFBS() doesn't require you to run getFootprints() first because getTFBS() will internally compute footprints for the required scales and use them to score TF binding. You can think of these two as parallel functionalities. In addition, if you take a look at our latest updated tutorial, I show an example of how to use getTFBindingSE() to load the TF binding scores of all candidate sites and pseudo-bulks into a combined SummarizedExperiment object. I hope this is helpful!