perform.tpm: Performs TPM normalisation

Description Usage Arguments Value Examples

View source: R/perform.tpm.normalisation.R

Description

Performs TPM normalisation, scran hvg selection, scaling and variance stabilisation and regression.

Usage

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perform.tpm(
  object,
  assay = "RAW",
  slot = "counts",
  n.genes = 1500,
  do.scale = FALSE,
  do.center = TRUE,
  vars.to.regress = NULL,
  new.assay.suffix = ""
)

Arguments

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

Value

Produces a new 'methods' assay containing normalised, scaled and HVGs.

Examples

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object <- perform.scanpy(object = object, 
                         vars.to.regress = 'RAW_total.counts', do.scale = T)

connorhknight/IBRAP_no_decontX documentation built on Feb. 13, 2022, 2:32 p.m.