How to reassign DESeqDataSet design to include newly added column to columnData
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rnavabjj • 0
@user-25125
Last seen 5 weeks ago

I would like to test for group-specific effects in my dataset. This contains a group, time and individual (ID) factors as is in the DESEQ2 Vignette under "Group-specific condition effects, individuals nested within groups". After adding a 'id.n' column to my dds, the vignette states:

"Now we can reassign our DESeqDataSet a design of ~ grp + grp:ind.n + grp:cnd, before we call DESeq. This new design will result in the following model matrix:"

It provides no information on reassigning the formula. I tried the following but the formula is linked to ibjects and this replaces it with language.

dds@design[[2]] <- 'group + group:ind.n+group:time'


Thank you for you help.

DESeq2 • 153 views
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@mikelove
Last seen 14 hours ago
United States

In Bioconductor, often there are dedicated "setter" and "getter" functions:

design(dds) <- ...


Another pointer, there is a way to see what functions are available for a specific object _and_ defined in a specific package, might be useful for you:

> showMethods(classes="DESeqDataSet", where=getNamespace("DESeq2"))

...

Function: design<- (package BiocGenerics)
object="DESeqDataSet", value="formula"
object="DESeqDataSet", value="matrix"

...


I was working at one point on trying to simplify retrieving this type of information, but haven't worked on it in a while:

https://rpubs.com/mikelove/pkgmethods

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Your timely response just saved my dissertation, Dr. Love. Thank you very much.