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YoannPa / methview.qc

HM450.QCView allows you to generate quality control plots from your Human Methylation 450K dataset.
GNU General Public License v3.0
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QC summary by sample #2

Closed AnjaCaRa closed 3 years ago

AnjaCaRa commented 3 years ago

It would be very helpful to have a function summarising the different quality control targets in terms of samples

YoannPa commented 3 years ago

I have create a first draft of the function requested. For now the function is still far from what it will optimally become, but more work is needed on the BiocompR dependence in order to make it happen.

So far the current version of the function devscore.heatmaps() produce 2 heatmaps of a deviation score relative to a reference for the intensities of fluorescence for HM450K quality control probes.

Using your data here is what can be produced for now:

dev.heatmaps <- devscore.heatmaps(
  RnBSet = result, target = "Hybridization", axis.text.x = element_text(
    size = 8, angle = -90, hjust = 0, vjust = 0.5, colour = "black"),
  axis.text.y.left = element_text(size = 10, colour = "black"))

Executing this chunk of code produces the heatmaps as shown below: 1 for the green channel, and another 1 for the red channel.

dev_heatmap_green dev_heatmap_red

An explanation of what this score is, and how it is calculated is available in the package help.
Again, we are still far from the definitive result, but this already allow to play around with samples, different targets and identify the faulty samples that should probably be excluded based on the QC data. One must be cautious about the interpretation as long as the development of the function is not done.

I suggest you to install the latest version of methview.qc in order to make use of this new function for your analysis.
This issue will remain open as long as the final result is not reached.

YoannPa commented 3 years ago

@AnjaCaRa The latest commit provide a suitable answer to this feature request. For any new request about options available in this function, please open a distinct issue. Good luck!