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Issue 59 #62

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Issue 59 #62

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e47b2d2
Fixed incorrect subsetting related to the coldata
StijnVandenbulcke May 7, 2024
ae55b18
Forgot a comma
StijnVandenbulcke May 7, 2024
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42 changes: 21 additions & 21 deletions R/msqrob-methods.R
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Original file line number Diff line number Diff line change
Expand Up @@ -103,32 +103,32 @@ setMethod(
"\' in the rowData of the SummarizedExperiment object, set the argument overwrite=TRUE to replace the column with the new results or use another name for the argument modelColumnName to store the results as a novel column in the rowData of SummarizedExperiment object"
)
}

if (length(formula) == 3) {
formula <- formula[-2]
}

if (any(all.vars(formula) %in% colnames(rowData(object)))){
stop(
"Use the msqrobAggregate function to use rowData variables"
)
}
#Get the variables from the formula and check if they are in the coldata or rowdata



#Get the variables from the formula and check if they are in the coldata or rowdata
check_vars <- all.vars(formula) %in% colnames(colData(object))
if (!all(check_vars)){
if(sum(!check_vars) >1) {
vars_not_found <- paste0(all.vars(formula)[!check_vars], collapse=", ")
stop(paste("Variables", vars_not_found, "are not found in coldata"), sep = "")
stop(paste("Variables", vars_not_found, "are not found in coldata"), sep = "")
} else{
vars_not_found <- all.vars(formula)[!check_vars]
stop(paste0("Variable ", vars_not_found, " is not found in coldata"), sep = "")
stop(paste0("Variable ", vars_not_found, " is not found in coldata"), sep = "")
}
}


if (!ridge & is.null(findbars(formula))) {
rowData(object)[[modelColumnName]] <- msqrobLm(
y = assay(object),
Expand All @@ -151,7 +151,7 @@ setMethod(
lmerArgs = lmerArgs
)
}

rowData(object)[[modelColumnName]] <- rowData(object)[[modelColumnName]][rownames(rowData(object))]
return(object)
}
Expand Down Expand Up @@ -186,42 +186,42 @@ setMethod(
"of the QFeatures object, set the argument overwrite=TRUE to replace the column with the new results or use another name for the argument modelColumnName to store the results as a novel column in the rowData of assay of the QFeatures object"
)
}

if (length(formula) == 3) {
formula <- formula[-2]
}

if (any(all.vars(formula) %in% colnames(rowData(object[[i]])))){
stop(
"Use the msqrobAggregate function to use rowData variables"
)
}
#Get the variables from the formula and check if they are in the coldata or rowdata

#Get the variables from the formula and check if they are in the coldata or rowdata
check_vars <- all.vars(formula) %in% colnames(colData(object))
if (!all(check_vars)){
if(sum(!check_vars) >1) {
vars_not_found <- paste0(all.vars(formula)[!check_vars], collapse=", ")
stop(paste("Variables", vars_not_found, "are not found in coldata"), sep = "")
stop(paste("Variables", vars_not_found, "are not found in coldata"), sep = "")
} else{
vars_not_found <- all.vars(formula)[!check_vars]
stop(paste0("Variable ", vars_not_found, " is not found in coldata"), sep = "")
stop(paste0("Variable ", vars_not_found, " is not found in coldata"), sep = "")
}
}

if (!ridge & is.null(findbars(formula))) {
rowData(object[[i]])[[modelColumnName]] <- msqrobLm(
y = assay(object[[i]]),
formula = formula,
data = droplevels(colData(object)),
data = droplevels(colData(getWithColData(object, i = i))),
robust = robust,
maxitRob = maxitRob
)
} else {
rowData(object[[i]])[[modelColumnName]] <- msqrobLmer(
y = assay(object[[i]]),
formula = formula,
data = droplevels(colData(object)),
data = droplevels(colData(getWithColData(object, i = i))),
rowdata = NULL,
robust = robust,
ridge = ridge,
Expand All @@ -231,7 +231,7 @@ setMethod(
lmerArgs = lmerArgs
)
}

rowData(object[[i]])[[modelColumnName]] <- rowData(object[[i]])[[modelColumnName]][rownames(rowData(object[[i]]))]
return(object)
}
Expand Down
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