normalize_data {hipathia} | R Documentation

## Normalize expression data from a SummarizedExperiment or matrix to be used in `hipathia`

### Description

Transforms the rank of the SummarizedExperiment or matrix of gene expression to [0,1] in order to be processed by `hipathia`. The transformation may be performed in two different ways. If `percentil = FALSE`, the transformation is a re-scaling of the rank of the matrix. If `percentil = TRUE`, the transformation is performed assigning to each cell its percentil in the corresponding distribution. This option is recommended for distributions with very long tails.

### Usage

    normalize_data(data, sel_assay = 1, by_quantiles = FALSE, by_gene = FALSE,
      percentil = FALSE, truncation_percentil = NULL)

### Arguments

`data` | Either a SummarizedExperiment or a matrix of gene expression.
`sel_assay` | Character or integer, indicating the assay to be normalized in the SummarizedExperiment. Default is 1.
`by_quantiles` | Boolean, whether to normalize the data by quantiles. Default is FALSE.
`by_gene` | Boolean, whether to transform the rank of each row of the matrix to [0,1]. Default is FALSE.
`percentil` | Boolean, whether to take as value the percentil of each sample in the corresponding distribution.
`truncation_percentil` | Real number p in [0,1]. When provided, values beyond percentil p are truncated to the value of percentil p, and values beyond 1-p are truncated to percentil 1-p. By default no truncation is performed.

### Details

This transformation may be applied either to the whole matrix (by setting `by_gene = FALSE`), which we strongly recommend, or to each of the rows (by setting `by_gene = TRUE`), allowing each gene to have its own scale.

A previous quantiles normalization may be applied by setting `by_quantiles = TRUE`. This is recommended for noisy data.

For distributions with extreme outlayer values, a percentil `p` may be given to the parameter `truncation_percentil`. When provided, values beyond percentil p are truncated to the value of percentil p, and values beyond 1-p are truncated to percentil 1-p. This step is performed before any other tranformation. By default no truncation is performed.

### Value

Matrix of gene expression whose values are in [0,1].

### Examples

    data("brca_data")
    trans_data <- translate_data(brca_data, "hsa")
    exp_data <- normalize_data(trans_data)
    exp_data <- normalize_data(trans_data, by_quantiles = TRUE,
    truncation_percentil=0.95)

[Package hipathia version 1.0.0 Index]