Applies normalization on sequencing data

Usage

ApplyNormalization(
  data,
  scaling.method = c("TC", "UQ", "TMM", "DESeq", "PossionSeq"),
  ruv.norm = TRUE,
  ruv.k = 1,
  ruv.drop = 0,
  control.idx = NULL,
  sc.idx = NULL,
  enrich.idx = NULL,
  spike.in.prefix = NULL,
  synthetic.id = NULL
)

Arguments

data: A un-normalized count data matrix of shape n x p, where n is the number of samples and p is the number of features.
scaling.method: Vector of normalization methods that are applied to the data. Available methods are: c("TC", "UQ", "TMM", "DESeq", "PossionSeq"). Select one or multiple methods. By default all normalization methods will be applied.
ruv.norm: Whether to perform RUV normalization.
ruv.k: The number of factors of unwanted variation to be estimated from the data.
ruv.drop: The number of singular values to drop in the estimation of unwanted variation, default drop the first singular value that represent the difference between enrichment and input.
control.idx: Vector of the negative control genes for RUV normalization.
sc.idx: A numeric matrix specifying the replicate samples for which to compute the count differences used to estimate the factors of unwanted variation.
enrich.idx: Matrix with two rows indicating the column index of enrichment and input samples in the raw/normalized count data matrix. The first row is the column index of input and the second row is the column index of enrichment samples.
spike.in.prefix: A character specify the prefix of spike-in id.
synthetic.id: Character or vector of string specifying the name of synthetic RNAs.

Value

List of objects containing normalized data and associated normalization factors.