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fix error when run revolver pipeline #47

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fix error when run revolver pipeline #47

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d87c7b8
fix error: when `drv_to_cancel` has only 0 length
Yunuuuu Dec 25, 2022
d4f3130
fix error when `p1_IT` or `p2_IT` is NULL
Yunuuuu Dec 25, 2022
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3 changes: 1 addition & 2 deletions R/remove_patients.R
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Original file line number Diff line number Diff line change
Expand Up @@ -46,10 +46,9 @@ remove_patients = function(x,

if(length(drv_to_cancel) > 0) {
message(paste(drv_to_cancel, collapse = ', '), ": driver events that now are found in only one patient, will be now removed ...")
x = remove_drivers(x, drv_to_cancel, check = FALSE)
}

x = remove_drivers(x, drv_to_cancel, check = FALSE)

# if has clusters, force to recompute
if(has_clusters(x)) {
message("- The cohort has clusters which will be cancelled, please re-compute the clusters ...")
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9 changes: 5 additions & 4 deletions R/revolver_cluster.R
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Expand Up @@ -83,11 +83,12 @@ revolver_cluster = function(
if (pb.status) pb$tick()$print()

# Both patient have a transfer that we take and augment with E
p1_IT = ITransfer(x, patients[p1], data = 'fits', type = 'drivers') %>%
left_join(E, by = c('from', 'to'))
p1_IT = ITransfer(x, patients[p1], data = 'fits', type = 'drivers')
if (!is.null(p1_IT)) p1_IT <- left_join(p1_IT, E, by = c('from', 'to'))

p2_IT = ITransfer(x, patients[p2], data = 'fits', type = 'drivers') %>%
left_join(E, by = c('from', 'to'))
p2_IT = ITransfer(x, patients[p2], data = 'fits', type = 'drivers')
if (!is.null(p2_IT)) p2_IT <- left_join(p2_IT, E, by = c('from', 'to'))


# The distance is the absolute value of non-shared edges
distances[patients[p1], patients[p2]] = bind_rows(p1_IT, p2_IT) %>%
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