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GreenleafLab / ChrAccR

Analyzing chromatin accessibility data in R
https://GreenleafLab.github.io/ChrAccR/
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TSS enrichment score #7

Closed banwang27 closed 2 years ago

banwang27 commented 2 years ago

Hi, I've been trying to use ChrAccR to evaluate my bulk ATAC-seq dataset. I notice that there are two types of TSS scores: getTssEnrichment(dsa, id)$tssEnrichment AND getTssEnrichment(dsa, id)$tssEnrichment.smoothed What's the difference between these two scores and which one we should mainly look at to follow ENCODE's criteria?

Also, I notice these two functions gives inconsistent results: 'getTssEnrichment(dsa, id)$tssEnrichment.smoothed' AND 'getTssEnrichmentBatch(dsa,sampleIds = getSamples(dsa))$tssEnrichment.smoothed'. Could you explain what's the difference? Thanks!

demuellae commented 2 years ago

Hi, tssEnrichment refers to the enrichment based on raw counts at each position around the TSS. the smoothed version is more commonly used (I believe also by ENCODE) and it does a window based smoothing of these raw counts. Hope that helps