new_cem: Create a CEMiTool object

In CEMiTool: Co-expression Modules identification Tool

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)

CEMiTool documentation built on March 13, 2021, 2 a.m.