Question

FourCseq, rawRanges Description

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Theo ▴ 10

@theodoregeorgomanolis-7993

Last seen 1 day ago

Germany

Hi Felix once more,

I am trying to figure out a few things on the R script and I wandering what the rawRanges holds.

I can extract the following items:
leftSize    rightSize    leftValid    rightValid    mid    dist    posLeft    posRight    blind    vpChr    tooClose    lowCounts    selectedForFit    baseMean    baseVar    allZero    dispGeneEst    dispFit    dispersion    dispIter    dispOutlier    dispMAP    Intercept    condition0min_Nat    condition60min_Nat    SE_Intercept    SE_condition0min_Nat    SE_condition60min_Nat    MLE_Intercept    MLE_condition_60min_Nat_vs_0min_Nat    WaldStatistic_Intercept    WaldStatistic_condition0min_Nat    WaldStatistic_condition60min_Nat    WaldPvalue_Intercept    WaldPvalue_condition0min_Nat    WaldPvalue_condition60min_Nat    betaConv    betaIter    deviance    maxCooks

Is it too much to ask what is each name represents?

Thank you for your help till now

fourcseq • 993 views

ADD COMMENT • link updated 7.7 years ago by felix.klein ▴ 150 • written 7.7 years ago by Theo ▴ 10

score 0 · Answer 1 · 2016-07-31

Hello Theodoros, these are a mixture from FourCSeq and DESeq2. For FourCSeq I can tell what they are, for DESeq2 you have to look it up in the documentation. leftSize/rightSize: Size of the left fragment end (1st to 2nd cutter site) leftValid/rightValid: Are the fragment ends valid (fragment of first cutter contains 2nd Cutter side and ends are large enough) mid: Middle of the fragment dist: Distance to the viewpoint fragment (middle to middle) posLeft/posRight: is the fragment left/right of the viewpoint blind: is it blind? vpChr: is it on the viewpoint chromosome? tooClose: to close to the viewpoint fragment? lowCounts: does the fragment fall below the count threshold? selectedForFit: was the fragment used for fitting the trend of the distance dependency? Hope this helps. Best regards, Felix