tomoMatrix {tomoda} | R Documentation

## Create an object from matrix

### Description

`tomoMatrix` creates an object from raw read count matrix or normalized read count matrix.

### Usage

    tomoMatrix(
      matrix.count = NULL,
      matrix.normalized = NULL,
      min.section = 3,
      normalize = TRUE,
      normalize.method = "median",
      scale = TRUE
    )

### Arguments

`matrix.count` | A numeric matrix or matrix-like data stucture that can be coverted to matrix, with genes with rows, sections as columns and values as raw read counts. Columns should be sorted according to section numbers.
`matrix.normalized` | A numeric matrix or matrix-like data stucture that can be coverted to matrix, with genes as rows, sections as columns and values as normalized read counts. Columns should be sorted according to order of sections.
`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)
    zh <- tomoMatrix(zh.data)

[Package tomoda version 1.0.0 Index]