scaling {SCdeconR}

Normalization of gene expression data

Description

Methods to use for data normalization.

Usage

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

Details

refer to scdecon for more details.

Value

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