tomoSummarizedExperiment {tomoda} | R Documentation

## Create an object from SummarizedExperiment

### Description

`tomoSummarizedExperiment` creates an object from a SummarizedExperiment object.

### Usage

    tomoSummarizedExperiment(
      se,
      min.section = 3,
      normalize = TRUE,
      normalize.method = "median",
      scale = TRUE
    )

### Arguments

`se` | A SummarizedExperiment object, it must contain at least one of 'count' assay and 'normalized' assay.
`min.section` | Integer. Genes expressed in less than `min.section` sections will be filtered out.
`normalize` | Logical, whether to perform normalization when creating the object. Default is TRUE.
`normalize.method` | Character, must be one of `"median"`, or `"cpm"`.
`scale` | Logical, whether to perform scaling when creating the object. Default is TRUE.

### Value

A `SummarizedExperiment` object

### See Also

`createTomo` for the generic function.

### Examples

    data(zh.data)
    se <- SummarizedExperiment::SummarizedExperiment(assays=list(count=zh.data))
    zh <- tomoSummarizedExperiment(se)

[Package tomoda version 1.0.0 Index]