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Blocking #57

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merged 7 commits into from
Oct 18, 2023
Merged

Blocking #57

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603e08e
added na.omit to assay reading
WackerO Oct 12, 2023
69392e0
making blocking column optional
WackerO Oct 17, 2023
779034b
Merge branch 'develop' of https://github.com/pinin4fjords/shinyngs in…
WackerO Oct 17, 2023
4e36ed0
Update R/accessory.R
WackerO Oct 17, 2023
cd2b4fe
Added conditional around blocking
WackerO Oct 17, 2023
052f461
fixed incorrect var names
WackerO Oct 17, 2023
94c68b3
Fix blocking conditionality
pinin4fjords Oct 17, 2023
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9 changes: 7 additions & 2 deletions R/accessory.R
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Original file line number Diff line number Diff line change
Expand Up @@ -913,7 +913,10 @@ read_contrasts <-
# Read the contrasts

contrasts <- read_metadata(filename)
contrast_cols <- c(variable_column, reference_column, target_column, blocking_column)
contrast_cols <- c(variable_column, reference_column, target_column)
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if (! blocking_column %in% names(contrasts)){
contrasts[[blocking_column]] <- NA
}

# Check contrast headers are as expected

Expand All @@ -927,7 +930,9 @@ read_contrasts <-

success <- checkListIsSubset(contrasts$variable, colnames(samples), "contrast variables", "sample metadata")

blocking <- unlist(lapply(contrasts$blocking, function(x) simpleSplit(x, ";")))
# Check blocking variables, where supplied

blocking <- unlist(lapply(contrasts[[blocking_column]], function(x) simpleSplit(x, ";")))
blocking <- blocking[!is.na(blocking)]
if (length(blocking > 0)) {
success <- checkListIsSubset(blocking, colnames(samples), "blocking variables", "sample metadata")
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