TSSEscore function in ATACseqQC package
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Liu Yu-Yu • 0
@e0215a8f
Last seen 3 months ago
Japan

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?

ATACseqQC • 441 views
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Hi Yu-Yu,

May I know the version of ATACseqQC? Thank you.

Jianhong.

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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

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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

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It is for all TSSs in the genome. TSS score is for each TSS.

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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?

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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.

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Now that makes sense! Thank you so much!