new_cem {CEMiTool} | R Documentation

## Create a CEMiTool object

### Description

Create a CEMiTool object

### Usage

    new_cem(
      expr = data.frame(),
      sample_annot = data.frame(),
      sample_name_column = "SampleName",
      class_column = "Class",
      filter = TRUE,
      apply_vst = FALSE,
      filter_pval = 0.1
    )

### Arguments

`expr` | Object of class `data.frame` with gene expression data
`sample_annot` | Object of `data.frame` containing the sample annotation. It should have at least two columns containing group Class and the Sample Name that should match with samples in expression file
`sample_name_column` | A string specifying the column to be used as sample identification. Default: "SampleName".
`class_column` | A string specifying the column to be used as a grouping factor for samples. Default: "Class"
`filter` | Logical. Used to define if posterior functions should use filtered expression data or not (Default: TRUE)
`apply_vst` | Logical. Used to define if posterior functions should use a variance stabilizing transformation on expression data before analyses. Only valid if argument `filter` is TRUE. (Default: FALSE)
`filter_pval` | logical. Threshold for filter p-value. Ignored if filter = FALSE (Default: 0.1)

### Value

Object of class `CEMiTool`

### Examples

    # Create new CEMiTool object
    cem <- new_cem()
    # Create new CEMiTool object with expression and sample_annotation data
    data(expr0)
    data(sample_annot)
    cem <- new_cem(expr0, sample_annot, "SampleName", "Class")
    # Equivalent to a call to new()
    cem2 <- new("CEMiTool", expression=expr0, sample_annotation=sample_annot)
    identical(cem, cem2)

[Package CEMiTool version 1.16.0 Index]