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msqrob()
Reproducible example:
se1 <- SummarizedExperiment(assays = matrix(100, 10, 10, dimnames = list(letters[1:10], LETTERS[1:10]))) se2 <- SummarizedExperiment(assays = matrix(50, 10, 5, dimnames = list(letters[1:10], LETTERS[6:10]))) cd <- DataFrame(foo = paste0("bar", rep(1:2, 5)), row.names = LETTERS[1:10]) qf <- QFeatures(experiments = List(set1 = se1, set2 = se2), colData = cd) msqrob(qf, i = "set1", formula = ~ foo) ## Works ok msqrob(qf, i = "set2", formula = ~ foo) ## Breaks msqrob(qf[, , "set2"], i = "set2", formula = ~ foo) ## Works ok
set2 contains a subset of samples in set1. The function breaks because de colData is not correctly retrieved here:
set2
set1
colData
msqrob2/R/msqrob-methods.R
Line 216 in 7b2399d
Line 224 in 7b2399d
I would suggest to first extract (within the msqrob()method) the set of interest with getWithColData(), which will automatically manage the colData.
getWithColData()
The text was updated successfully, but these errors were encountered:
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Reproducible example:
set2
contains a subset of samples inset1
. The function breaks because decolData
is not correctly retrieved here:msqrob2/R/msqrob-methods.R
Line 216 in 7b2399d
msqrob2/R/msqrob-methods.R
Line 224 in 7b2399d
I would suggest to first extract (within the
msqrob()
method) the set of interest withgetWithColData()
, which will automatically manage thecolData
.The text was updated successfully, but these errors were encountered: