process_raw_scseq | R Documentation |
Performs the following: - normalization - adds HVGs - dimensionality reduction - clustering
process_raw_scseq(
scseq,
dataset_name,
sc_dir,
tx2gene_dir,
cluster_alg = "leiden",
npcs = 30,
resoln = 1,
hvgs = NULL,
ref_name = NULL,
founder = NULL,
progress = NULL,
value = 0
)
scseq |
|
dataset_name |
Name of dataset to save |
sc_dir |
Directory to save dataset to |
tx2gene_dir |
Path to directory containing transcript to gene maps produced by load_tx2gene. |
cluster_alg |
Cluster algorith. Either |
npcs |
Number of principal components to use. Default is 30. |
resoln |
|
hvgs |
Character vector of a priori genes to use for PCA. If |
ref_name |
Name of symphony or Azimuth reference to use for reference-based analysis. |
founder |
Name of original founding dataset (may be ancestor of |
progress |
Shiny progress object. Default ( |
value |
Initial value of progress. |
Then calls run_post_cluster
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