Description Usage Arguments Value Examples
View source: R/perform.tpm.normalisation.R
Performs TPM normalisation, scran hvg selection, scaling and variance stabilisation and regression.
1 2 3 4 5 6 7 8 9 10 | perform.tpm(
object,
assay = "RAW",
slot = "counts",
n.genes = 1500,
do.scale = FALSE,
do.center = TRUE,
vars.to.regress = NULL,
new.assay.suffix = ""
)
|
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 |
n.genes |
Numerical. Top number of genes to retain when finding HVGs. Default = 1500 |
do.scale |
Boolean. Whether to scale the features variance. Default = TRUE |
vars.to.regress |
Character. Which column in the metadata should be regressed. Default = NULL |
new.assay.suffix |
Character. What should the new assay be called. Default = 'SCRAN' |
do.centre |
Boolean. Whether to centre features to zero. Default = TRUE |
Produces a new 'methods' assay containing normalised, scaled and HVGs.
1 2 | object <- perform.scanpy(object = object,
vars.to.regress = 'RAW_total.counts', do.scale = T)
|
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