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v1.3.0 release #64

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Merged
jfallmann merged 2 commits into from
Apr 1, 2026
+4 −8
Merged

v1.3.0 release #64

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3354117
edger cleanup
jfallmann Apr 1, 2026
8f11c74
Merge branch 'main' into dev_2.0
jfallmann Apr 1, 2026
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3 changes: 1 addition & 2 deletions scripts/Analysis/DAS/EDGER.R
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Expand Up @@ -245,8 +245,7 @@ for (compare in comparisons[[1]]) {
# }
# contrast <- as.numeric(contrast[,1])

# create files topSpliced by gene, simes and exon method
# sp <- diffSpliceDGE(fit, contrast=contrast, geneid="genes", exonid="exons", verbose=FALSE)
# create files topSpliced by gene, simes and exon method
sp <- diffSpliceDGE(fit, geneid = "genes", exonid = "exons", verbose = FALSE)

# add comp object to list for image
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4 changes: 1 addition & 3 deletions scripts/Analysis/DE/EDGER.R
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Expand Up @@ -318,9 +318,7 @@ for (contrast in comparison[[1]]) {
# contrast[which(contrast[,2]==i)]<- plus
# }
# contrast <- as.numeric(contrast[,1])

## Testing
# qlf <- glmQLFTest(fit, contrast=contrast) ## glm quasi-likelihood-F-Test

AvsB <- makeContrasts(TreatvsUntreat = paste("condition", A, sep = ""), levels = design)
qlf <- glmQLFTest(fit, contrast = AvsB, prior.count = 5) ## glm quasi-likelihood-F-Test
# add comp object to list for image
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5 changes: 2 additions & 3 deletions scripts/Analysis/DEU/EDGER.R
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Expand Up @@ -239,9 +239,8 @@ for (compare in comparisons[[1]]) {
# }
# contrast <- as.numeric(contrast[,1])

# quasi-likelihood F-Test
# qlf <- glmQLFTest(fit, contrast = contrast)
qlf <- glmQLFTest(fit, prior.count = 5)
# quasi-likelihood F-Test
qlf <- glmQLFTest(fit)
is.de <- decideTests(qlf, p.value = 0.05)

# add comp object to list for image
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