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,
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,