sample_annotation {CEMiTool} | R Documentation

## Retrive or set the sample_annotation attribute

### Description

Retrive or set the sample_annotation attribute

### Usage

    sample_annotation(cem)

    ## S4 method for signature 'CEMiTool'
    sample_annotation(cem)

    sample_annotation(
      cem,
      sample_name_column = "SampleName",
      class_column = "Class"
    ) <- value

    ## S4 replacement method for signature 'CEMiTool'
    sample_annotation(
      cem,
      sample_name_column = "SampleName",
      class_column = "Class"
    ) <- value

### Arguments

`cem` | Object of class `CEMiTool`
`sample_name_column` | A string containing the name of a column which should be used as a unique identifier for samples in the file. Only used when assigning a sample annotation data.frame. Default: "SampleName".
`class_column` | A string containing the name of a column which should be used to identify different sample groups. Only used when assigning a sample annotation data.frame. Default: "Class"
`value` | A data.frame containing the sample annotation, should have at least two columns containing the Class and the Sample Name that should match with samples in expression

### Value

A data.frame containing characteristics of each sample.

### Examples

    # Get example expression data
    data(expr0)
    # Get example sample_annotation data
    data(sample_annot)
    # Initialize CEMiTool object with expression
    cem <- new_cem(expr0)
    # Add sample annotation file to CEMiTool object
    sample_annotation(cem,
        sample_name_column="SampleName",
        class_column="Class") <- sample_annot
    # Check annotation
    head(sample_annotation(cem))

[Package CEMiTool version 1.18.1 Index]