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Guard MannKendall against segments with <3 non-NA values #10

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Guard MannKendall against segments with <3 non-NA values #10

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21 changes: 20 additions & 1 deletion R/cellcycle.R
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Original file line number Diff line number Diff line change
Expand Up @@ -59,11 +59,24 @@ cellcycleMetadata <- function(segmentedCounts,segment_size_cutoff=20){
return(list("pval"=NA, "tau"=NA, "tau_corrected"=NA, "cor_corrected"=NA))
}
co = counts[index == x]
if(all(co == 0)){
if(all(co == 0, na.rm=TRUE)){
return(list("pval"=NA, "tau"=NA, "tau_corrected"=NA, "cor_corrected"=NA))
}
time = repTime[index == x]
covar = gc_map_covariate[index == x]
# Mann-Kendall (and the partial-MK / partial-spearman calls below) all
# need >=3 jointly-non-NA values. With aggressive mouse filtering
# (blacklist + pericentromeric + segdup) and mm10-liftover gaps in
# the replication-timing track, a long segment can clear the size
# cutoff but still have <3 bins that are non-NA across co, time and
# covar simultaneously. base::sort(time, ...) drops NAs from time
# silently, so the resulting idx is shorter than the segment and
# co[idx] feeds a degenerate vector into Kendall::MannKendall,
# triggering stop("length(x)<3") inside the package.
jointly_valid = !is.na(co) & !is.na(time) & !is.na(covar)
if(sum(jointly_valid) < 3){
return(list("pval"=NA, "tau"=NA, "tau_corrected"=NA, "cor_corrected"=NA))
}
idx = base::sort(time, index.return=TRUE)$ix
# ggplot(data=dplyr::tibble(co=co[idx], covar=covar[idx], time=time[idx])) + geom_point(aes(x=time, y=co, color=covar))
trend.kendall_test = Kendall::MannKendall(co[idx])
Comment on lines +67 to 82
Expand Down Expand Up @@ -186,6 +199,12 @@ cellcycle_gctest <- function(segmentedCounts, segment_size_cutoff=20){
}
co = counts[index == x]
time = gc[index == x]
# See cellcycleMetadata above for the same guard. base::sort(time, ...)
# silently drops NA time values, so the segment can clear the size
# gate but still feed a <3-length vector to Kendall::MannKendall.
if(sum(!is.na(co) & !is.na(time)) < 3){
return(list("pval"=NA, "tau"=NA))
}
idx = base::sort(time, index.return=TRUE)$ix
trend.kendall_test = Kendall::MannKendall(co[idx])
Comment on lines +202 to 209
pv = trend.kendall_test[["sl"]][[1]]
Expand Down