Normalization of gene expression data

Methods to use for data normalization.

scaling(
  matrix,
  option,
  gene_length = NULL,
  seed = 1234,
  ffpe_artifacts = FALSE,
  model = NULL
)

Arguments

matrix: a matrix-like objector of gene expression values with rows representing genes, columns representing samples or cells
option: character value specifying the normalization method to use. Has to be one of "none", "LogNormalize", "TMM", "median_ratios", "TPM", "SCTransform", "scran", "scater", "Linnorm".
gene_length: a data.frame with two columns. The first column represents gene names that match with provided bulk data. The second column represents length of each gene. Only applicable when norm_method is selected as "TPM"
seed: random seed used for simulating FFPE artifacts. Only applicable when ffpe_artifacts is set to TRUE.
ffpe_artifacts: logical value indicating whether to add simulated ffpe artifacts in the bulk data. Only applicable to simulation experiments in evaluating the effect of FFPE artifacts.
model: pre-constructed ffpe model data. Can be downloaded from github: https://github.com/Liuy12/SCdeconR/blob/master/data/ffpemodel.rda

a matrix-like object with the same dimension of input object after data normalization.

refer to scdecon for more details.