You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Running the below code on a large reference and run into the error in the title. Any ideas on a fix would be greatly appreciated,
set.seed(0)
full_reference = symphony::buildReference(
normalized_counts,
metadata,
vars = c('donor_id'), # variables to integrate over
K = 100, # number of Harmony clusters
verbose = TRUE, # verbose output
do_umap = TRUE, # can set to FALSE if want to run umap separately later
do_normalize = FALSE, # set to TRUE if input counts are not normalized yet
vargenes_method = 'vst', # method for variable gene selection ('vst' or 'mvp')
vargenes_groups = 'annotation_20230508', # metadata column specifying groups for variable gene selection
topn = 2000, # number of variable genes to choose per group
d = 20, # number of PCs
save_uwot_path = 'toncil_full_reference_uwot'
)
Cheers,
The text was updated successfully, but these errors were encountered:
Running the below code on a large reference and run into the error in the title. Any ideas on a fix would be greatly appreciated,
set.seed(0)
full_reference = symphony::buildReference(
normalized_counts,
metadata,
vars = c('donor_id'), # variables to integrate over
K = 100, # number of Harmony clusters
verbose = TRUE, # verbose output
do_umap = TRUE, # can set to FALSE if want to run umap separately later
do_normalize = FALSE, # set to TRUE if input counts are not normalized yet
vargenes_method = 'vst', # method for variable gene selection ('vst' or 'mvp')
vargenes_groups = 'annotation_20230508', # metadata column specifying groups for variable gene selection
topn = 2000, # number of variable genes to choose per group
d = 20, # number of PCs
save_uwot_path = 'toncil_full_reference_uwot'
)
Cheers,
The text was updated successfully, but these errors were encountered: