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kvittingseerup / IsoformSwitchAnalyzeR

An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
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comparisonsToMake wiith 4four conditions #234

Closed rvermamsm closed 3 months ago

rvermamsm commented 3 months ago

Hello

I have 4 conditions in my data. Can I compare them like this:

comparisons_to_make <- as.data.frame( rbind( c("Disc_NO", "Base_NO"), c("4-6h_NO", "Base_NO"), c("Disc_YES", "Base_YES"), c("4-6h_YES", "Base_YES") ), stringsAsFactors = FALSE # Ensure that strings are not converted to factors )

Rename columns to match the expected format

colnames(comparisons_to_make) <- c("condition_1", "condition_2")

Import data with additional comparisons

aSwitchList_str <- importRdata( isoformCountMatrix = stringQuant$counts, isoformRepExpression = stringQuant$abundance, designMatrix = myDesign, isoformExonAnnoation = gtf, isoformNtFasta = NULL, showProgress = FALSE, ignoreAfterBar = TRUE, ignoreAfterSpace = TRUE, addAnnotatedORFs = TRUE, ignoreAfterPeriod = FALSE, comparisonsToMake = comparisons_to_make )

Is this the correct way to compare all this condition at a time?

chunxubioinfor commented 3 months ago

Hi, I think it's the right way to achieve the four comparisons. But I recommend you put baseline as condition 1 and case as condition 2 (if this Base means baseline), which will enable the following visualisation to be more intuitive.

rvermamsm commented 3 months ago

Thank you for your quick response.