I am applying ATACseqQC on my mouse data, but failed to run TSSEscore function.
For the moment, all the following functions worked well: estimateLibComplexity, fragSizeDist, shiftGAlignmentsList, splitGAlignmentsByCut, estLibSize, featureAlignedHeatmap, featureAlignedDistribution and gave reasonable results.
But when I used TSSEscore as written in the manual:
tsse <- TSSEscore(gal1, txs) tsse$TSSEscore  NULL
As you see tsse$TSSEscore did not exist and returned NULL. But when I look into tsse:
tsse$ tsse$TSS.enrichment.score tsse$flank.mean tsse$tx-id tsse$TSS.mean tsse$id tsse$tx_name
Does anyone has any idea why the TSSEscore for all TSS was not calculated? How exactly does this function works?