sce_norm_hvg_fn | R Documentation |
Prior to HVG selection, cell cycle-related gene can be removed.
For more details see the HVG selection section in 02_norm_clustering.yaml
config.
sce_norm_hvg_fn(
sce_norm,
hvg_selection_value,
hvg_metric = c("gene_var", "gene_cv2", "sctransform"),
hvg_selection = c("top", "significance", "threshold"),
hvg_rm_cc_genes = FALSE,
hvg_cc_genes_var_expl_threshold = 5,
BSPARAM = BiocSingular::IrlbaParam(),
BPPARAM = BiocParallel::SerialParam()
)
sce_norm |
(input target) A |
hvg_selection_value, hvg_metric, hvg_selection |
Passed to |
hvg_rm_cc_genes |
A logical scalar: if |
hvg_cc_genes_var_expl_threshold |
A numeric scalar: threshold for variance explained. Genes exceeding this threshold will be marked as CC-related. |
BSPARAM |
A BiocSingular::BiocSingularParam object. |
BPPARAM |
A BiocParallel::BiocParallelParam object. |
A modified sce_norm
object with added HVG data in metadata()
.
Output target: sce_norm_hvg
The following items of metadata(sce_norm)
are added or modified:
hvg_metric
, hvg_selection
, hvg_selection_value
, hvg_rm_cc_genes
, hvg_cc_genes_var_expl_threshold
:
values passed to the function.
hvg_metric_fit
: either DataFrame
returned from scran::modelGeneVar()
or scran::modelGeneCV2()
,
or feature.attributes
dataframe returned from Seurat::SCTransform()
.
Values added by sce_remove_cc_genes()
.
hvg_ids
: a character vector of HVG ENSEMBL IDs.
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