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mansuylab / SC_postnatal_adult

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TFA analysis #8

Open plger opened 5 years ago

plger commented 5 years ago

Transcript factor activity analysis

Give a SE object and a DEA:

library(plgINS)
data(regulon.curated.mm)
regulon <- regulon.filter(regulon.curated.mm)
vi <- TFA(SE, DEA, design=~Condition, regulon=regulon)
plotTFA(vi)
sehm(vi[1:20,],  anno_columns = c("Condition"), scale="row")

(if you test for more than one coefficient, use the testCoef parameter of TFA to specify)

dktanwar commented 5 years ago

Hi @plger

What is the meaning of all these:

activity.logFC: activity.meanActivity: activity.PValue: activity.FDR: expression.logFC: Taken from differential analysis? expression.PValue: Taken from differential analysis? expression.FDR: Taken from differential analysis? nbTargets: No. of target genes by this TF? nbTargetsInDEGs: No. of target genes by this TF which are also identified as differentially expressed? targetEnrichment: targetEnrFDR: DEtargets:

In the volcano plot plotTFA, which values are used for size of circles?

Which values are used for plotting heatmap?