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RitchieLabIGH / IRFinder

MIT License
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Feature request: Further output #10

Closed jscaber closed 2 years ago

jscaber commented 2 years ago

Dear Claudio,

would you consider adding a further output with individual IRratios for each sample +/- mean absolute IRratio (i.e. the data for plotting the graphs in the pdf)? The log2Foldchange is helpful but has limitations as it is not as biologically relevant.

Or should I be using SUPPA? Jakub

CloXD commented 2 years ago

Hello Jakub, it sounds a good idea, I'll work on it. Cheers, Claudio

CloXD commented 2 years ago

Hello Jakub, I've included an extended output including the IRratios of each sample, the means and the pairwise padj, baseMean and log2FoldChange from DESeq2. The output looks something like this: 

ID  IRratio.sample_1    IRratio.sample_2    IRratio.sample_3    IRratio.sample_4    IRratio.sample_5    IRratio.sample_6    MINUS.Mean.IRratio  PLUS.Mean.IRratio   DESeq2.padj.MINUS_PLUS  DESeq2.baseMean.MINUS_PLUS  DESeq2.log2FoldChange.MINUS_PLUS
ENSG00000188976;clean;1:954082-955922   0.036630036630037   0.05984555984556    0.029239766081871   0.034805890227577   0.041254125412541   0.041916167664671   0.041905120852489   0.03932539443493    0.981150057313931   300.166666666667    0.067437015661994
ENSG00000188976;clean;1:954523-955922   0.031307550644567   0.052529182879377   0.026392961876833   0.029609690444145   0.034883720930233   0.036144578313253   0.036743231800259   0.033545996562544   0.968339876337105   298.5   0.111073861609927
ENSG00000188976;clean;1:957273-958928   0.030131826741996   0.041025641025641   0.036053130929791   0.037795275590551   0.048837209302326   0.061611374407583   0.035736866232476   0.04941461976682    0.807282417860924   260.833333333333    -0.428854820392939
ENSG00000187961;clean;1:961750-961825   0.241379310344828   0.394736842105263   0.208333333333333   0.2 0.05    0.083333333333333   0.281483161927808   0.111111111111111   0.682993438221315   14  1.33984991816247
ENSG00000187961;clean;1:963253-963336   0.433333333333333   0.583333333333333   0.35    0.428571428571429   0.291666666666667   0.466666666666667   0.455555555555556   0.395634920634921   0.911116884374037   13.9166666666667    0.480409156882619
ENSG00000187961;clean;1:963504-963919   0.6 0.743589743589744   0.540540540540541   0.71875 0.769230769230769   0.645161290322581   0.628043428043428   0.71104735318445    0.89083006372948    15.8333333333333    -0.48629282594783

There is all the information to reproduce the graphs in the pdf. I generated a new tag for this version to keep it separated from the one of the publication. Cheers, Claudio

jscaber commented 2 years ago

Fantastic, thank you so much for this - very kind! Sorry for the delayed reply.