Get standardized omics data

This function prepare standardized data for generating heatmap. Omics data, especially for expression, should be centered or scaled or z-scored (both centered and scaled). Generally, DNA methylation beta matrix and somatic mutation (0 and 1 binary matrix) should not be normalized. This function also provides an argument of halfwidth for continuous omics data; such argument is used to truncate the 'extremum' after normalization; specifically, normalized values that exceed the halfwidth boundaries will be replaced by the halfwidth, which is vary useful to map colors in heatmap. Function adapted from package MOVICS (see ref)

getStdiz(
  data = NULL,
  halfwidth = rep(1, length(data)),
  centerFlag = rep(TRUE, length(data)),
  scaleFlag = rep(TRUE, length(data))
)

Arguments

data

A list of data.frame or matrix storing raw multiple omics data with rows for features and columns for samples.

halfwidth

A numeric vector to assign marginal cutoff for truncating values in data; 1 by default.

centerFlag

A logical vector to indicate if each subdata should be centered; TRUE by default.

scaleFlag

A logical vector to indicate if each subdata should be scaled; TRUE by default.

Value

A standardized data.frame containing multi-omics data.

References

Lu, X., et al. (2020). MOVICS: an R package for multi-omics integration and visualization in cancer subtyping. Bioinformatics, 36(22-23), 5539–5541.

See also

Other Plotting: circular_corrplot(), communities_network(), community_graph(), correlation_heatmap_clusters(), correlation_heatmap_supervised(), correlation_heatmap(), interactive_network(), multiomics_heatmap(), plot_OpenTarget(), plot_communities(), plot_components(), plot_loadings(), plot_optimal_cluster(), visualise_pathway(), volcano_interactive_comparison(), volcano_interactive(), volcano_plot_deseq(), volcano_plot_limma()