aucprTestByFactor

[MedCYLIU]

I'm a newbie in R and here I've run through URD with a single cell dataset, just like in https://github.com/farrellja/URD/issues/8#issue-340418955. I have a same question.

cm_fb <- cellsInCluster(object, "segment", c("4","1","3")) ec <- cellsInCluster(object, "segment", "2") groups <- list( c("HE05W", "HE06W"), c("HE07W", "HE09W"), c("HE13W", "HE17W"), c("HE20W", "HE22W"), c("HE23W", "HE24W", "HE25W") )

Then I followed your comments to check

class(object@group.ids$stage) [1] "character" table(object@group.ids$stage)

HE05W HE06W HE07W HE09W HE13W HE17W HE20W HE22W HE23W HE24W HE25W 307 236 429 94 231 95 47 265 67 123 18

I check the number of cells from each group in populations:

table(object@group.ids[cellsInCluster(object, "segment", c(4,1,3)), "stage"])

HE05W HE06W HE07W HE09W HE13W HE17W HE20W HE22W HE23W HE24W HE25W 216 61 308 46 188 61 20 205 40 77 2

table(object@group.ids[cellsInCluster(object, "segment", c(2)), "stage"])

HE05W HE06W HE07W HE09W HE13W HE17W HE20W HE22W HE23W HE24W HE25W 91 138 74 40 19 16 13 25 8 46 8

but when I run the

cm_fbvsec.markers.bystage <- aucprTestByFactor(object, cells.1=cm_fb, cells.2=ec,

• label="STAGE", groups=groups,
• log.effect.size=0.5, auc.factor=1, min.auc.thresh=0.1, max.auc.thresh=Inf,
• frac.must.express=0.1, frac.min.diff=0, genes.use=genes.use, min.groups.to.mark=3, report.debug=T) Error in [<-.data.frame(*tmp*, is.na(genes.data$AUCPR), "AUCPR", value = 0) : replacement has 1 row, data has 0

still I have.