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bartongroup / Proteus

R package for analysing proteomics data
MIT License
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Dealing with peptides/proteins that aren't detected in all conditions... #6

Closed nickschurch closed 6 years ago

nickschurch commented 7 years ago

Proteus really needs to have a good way of dealing with proteins and/or peptides that are not detected in one or more of the conditions. Currently, Proteus includes these data int he data import by limmaDE will not report a fold-change or a significance for them, nor will they be reported in the list of SDE molecules, and not will they be present on the volcano/fold-change-intensity plots that result. For some experiments (notably those involving an IP pulldown) these results are critical tot he experiment and are, arguably, the strongest evidence in the data.

I suggest computing a boolean table describing whether each peptide or protein is detected in each condition and adding this to both the peptide and protein tables (computed during makePeptideTable & makeProteinTable). This can then be easily use to index peptides/proteins detected/undetected in any combination of conditions (a/several functions for this would be useful too). In conjunction with the limmaDE results, these proteins/peptides can also be reported in the SDE list and cal also be added to the plots as points pegged to one/more axes and labelled with a different colour.

MarekGierlinski commented 7 years ago

Partially done. Added detect field to protein/peptide object with a logical table indicating detection in each condition. Updated the vignette as well. Will deal with plots later.

MarekGierlinski commented 6 years ago

From version 0.1.8 plotFID takes data present in only one into account. They are now shown (only in binhex=FALSE mode) as orange points at the top and bottom of the plot. This is not possible in plotVolcano as these data lack both p-value and fold change.