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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$TSSEscore
[1] NULL
As you see tsse$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?
Hi Yu-Yu,
May I know the version of ATACseqQC? Thank you.
Jianhong.
Hi Jianhong,
Thanks for the reply. I just realized that I actually had version 1.10.4 installed instead of the newest 1.18.0. The problem is solved! Thank you so much.
Yu-Yu
Hi Jianhong,
Sorry for bothering again. I am actually still quite confused for how ATACseqQC calculates the TSSEscore. In the manual, it is written that TSSE score = max(mean(TSS score in each window)). Is this the score for one single TSS or for all TSSs in the genome?
Yu-Yu
It is for all TSSs in the genome. TSS score is for each TSS.
Thanks for the explanation! But I thought that TSSEscore for all TSSs should represent the TSS scores for all TSSs, so I thought that it would be the average or median of all scores? What is the reason to use max?
Sorry for the confusion. The TSS scores are scores for the accumulation of each TSSs in each window. Here_Enrichment_Score) should have a better explanation.
Now that makes sense! Thank you so much!