FourCseq, rawRanges Description
Entering edit mode
Last seen 14 months ago
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 • 533 views
Entering edit mode
felix.klein ▴ 150
Last seen 3.1 years ago
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
Entering edit mode

Hi Felix,

I will look at them and come back to you.

Thank you again for your help


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