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Data normalization

data.normalization.Rd

Conduct normalization for dataset.

Usage

data.normalization(Data, type = "feature_Median", log2 = FALSE)

Arguments

Data

A matrix representing the genomic data such as gene expression data, miRNA expression data.
For the matrix, the rows represent the genomic features, and the columns represent the samples.

type

A character value representing the normalization type. The optional values are shown below:

  • "feature_Median". The default value. Normalize dataset by sweeping the median values of each feature.

  • "feature_Mean". Normalize dataset by sweeping the mean values of each feature.

  • "feature_zscore". Conduct z_score normalization for each feature.

  • "sample_zscore". Conduct z_score normalization for each samples.

log2

A logical value. If TRUE, the data is transform as log2(x+1). This is commonly used for RNAseq data.

Value

The normalized data matrix.

References

Xu T, Le TD, Liu L, Su N, Wang R, Sun B, Colaprico A, Bontempi G, Li J. CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization. Bioinformatics. 2017 Oct 1;33(19):3131-3133. doi: 10.1093/bioinformatics/btx378. PMID: 28605519.

Examples

data(mRNAexp)
result=data.normalization(mRNAexp,type="feature_Median",log2=FALSE)