Description Usage Arguments Value Examples
View source: R/perform.scanpy.normalisation.R
A new method-assay is produced. Raw counts are normalised and HVGs identified using Scanpy
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | 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
)
|
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 |
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.
1 2 | object <- perform.scanpy(object = object,
vars.to.regress = 'RAW_total.counts')
|
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