new_cem {CEMiTool} | R Documentation |
Create a CEMiTool object
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 )
expr |
Object of class |
sample_annot |
Object of |
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_pval |
logical. Threshold for filter p-value. Ignored if filter = FALSE (Default: 0.1) |
Object of class CEMiTool
# 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)