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Description
Hi, I had problem when I tried to run unifiedClusterLabelling function
my code is
batch.cluster.labels <- unifiedClusterLabelling(batches = list(ifnb.list[[1]]@assays$RNA, ifnb.list[[2]]@assays$RNA, ifnb.list[[3]]@assays$RNA),features.use = markers, cluster.labels = cluster.info, min.perc = 0.1)
But it errors, showning
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Computing nearest neighbor graph
Computing SNN
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Computing nearest neighbor graph
Computing SNN
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Computing nearest neighbor graph
Computing SNN
Error in for (i in x1) { : invalid for() loop sequence
In addition: Warning messages:
1: In type.convert.default(X[[i]], ...) :
'as.is' should be specified by the caller; using TRUE
2: In type.convert.default(X[[i]], ...) :
'as.is' should be specified by the caller; using TRUE
3: In type.convert.default(X[[i]], ...) :
'as.is' should be specified by the caller; using TRUE
4: In type.convert.default(X[[i]], ...) :
'as.is' should be specified by the caller; using TRUE
5: In cbind(group.index, index) :
number of rows of result is not a multiple of vector length (arg 2)
6: In cbind(group.index, index) :
number of rows of result is not a multiple of vector length (arg 2)
7: In group.assigned[i] <- cluster.multi_assigned[which(dist.i == min(dist.i))] :
number of items to replace is not a multiple of replacement length