This is my first post on here, and I haven't been able to find any other examples of problems with Outrider so far. I'm still hopeful someone might have the smarts to help me solve this issue.
I'm trying to run my very first OUTRIDER script in RStudio, but I keep getting an error message saying one of the functions cannot be found. Can anyone advise what might be causing this error or what might work to fix it?
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
ctsFile <- "OTRDGTEX2.txt"
ctsTable <- read.table(ctsFile, check.names=FALSE) ods <- OutriderDataSet(countData=ctsTable)
filter out non expressed genes
ods <- filterExpression(ods, minCounts=TRUE, filterGenes=TRUE)
run full OUTRIDER pipeline (control, fit model, calculate P-values)
ods <- OUTRIDER(ods)
ctsFile <- "OTRDGTEX2.txt" ctsTable <- read.table(ctsFile, check.names=FALSE) ods <- OutriderDataSet(countData=ctsTable) Error in OutriderDataSet(countData = ctsTable) : could not find function "OutriderDataSet"