aucprTestByFactor

[MedCYLIU]

I'm a newbie in R and here
I've run through URD with a single cell dataset, just like in #8 (comment). 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.