getStdiz: Get standardized omics data

In xlucpu/MOVICS: Multi-Omics integration and VIsualization in Cancer Subtyping

Description

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.

Usage

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.

Examples

# There is no example and please refer to vignette.

xlucpu/MOVICS documentation built on July 24, 2021, 9:23 p.m.