View source: R/perform.scanpy.normalisation.R
perform.scanpy | R Documentation |
A new method-assay is produced. Raw counts are normalised and HVGs identified using Scanpy
perform.scanpy( object, assay = "RAW", slot = "counts", new.assay.suffix = "", target_sum = 10000, exclude_highly_expressed = FALSE, max_fraction = 0.05, key_added = "scanpy_norm_factor", log1 = TRUE, n_top_genes = NULL, max_mean = 6, min_mean = 0.0125, min_disp = 0.5, span = 0.3, n_bins = 20, flavor = "seurat", batch_key = NULL, vars.to.regress = NULL, verbose = FALSE, seed = 1234 )
object |
IBRAP S4 class object |
assay |
Character. String containing indicating which assay to use |
slot |
Character. String indicating which slot within the assay should be sourced |
new.assay.suffix |
Character. What should be added as a suffix to 'SCANPY |
target_sum |
Numerical. What should the data be scaled to. Default = 1e6 |
exclude_highly_expressed |
Boolean. Should highly expressed genes be excluded. Default = FALSE |
max_fraction |
Numerical. If exclude_highly_expressed=True, consider cells as highly expressed that have more counts than max_fraction of the original total counts in at least one cell. Default = 0.05 |
key_added |
Character. What should the column name be that contains cell scaling factors. Default = 'scanpy_norm_factor' |
n_top_genes |
Numerical. How many HVGs should be identified. Default = NULL |
max_mean |
Numerical. If n_top_genes is NULL, this is the maximum mean to determine HVGs. Default = 6 |
min_mean |
Numerical. If n_top_genes is NULL, this is the minimum mean to determine HVGs. Default = 0.0125 |
min_disp |
Numerical. If n_top_genes is NULL, The minimum dispersion that should be presented in a gene for it to be considered highly varaible. Default = 0.5 |
span |
Numerical. The fraction of cells that should be subset for the LOESS fit model. Default = 0.3 |
n_bins |
Numerical. Number of bins to produce when determining HVGs |
batch_key |
Character. Which column in the metadata identifies the batches of the cells. Default = NULL |
vars.to.regress |
Character. A single or multiple columns of information in the metadata that should be regressed from the dataset. Default = NULL |
verbose |
Logical Should function messages be printed? |
seed |
Numerical What seed should be set. Default = 1234 |
flavour |
Character. Choosing which HVG selection method to use when, options: 'seurat', 'cell_ranger', 'seurat_v3'. Default = 'seurat' |
Produces a new 'methods' assay containing normalised, scaled and HVGs.
object <- perform.scanpy(object = object, vars.to.regress = 'RAW_total.counts')
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.