design,experiment-method {ORFik} | R Documentation

## Get experimental design Find the column/columns that create a separation between samples, by default skips replicate and choose first that is from either: libtype, condition, stage and fraction.

### Description

Get experimental design Find the column/columns that create a separation between samples, by default skips replicate and choose first that is from either: libtype, condition, stage and fraction.

### Usage

    ## S4 method for signature 'experiment'
    design(
      object,
      batch.correction.design = FALSE,
      as.formula = FALSE,
      multi.factor = TRUE
    )

### Arguments

`object` | an ORFik `experiment`
`batch.correction.design` | logical, default FALSE. If true, add replicate as a second design factor (only if >= 2 replicates exists).
`as.formula` | logical, default FALSE. If TRUE, return as formula
`multi.factor` | logical, default TRUE If FALSE, return first factor only (+ rep, if batch.correction.design is true). Order of picking is: libtype, if not then: stage, if not then: condition, if not then: fraction.

### Value

a character (name of column) or a formula

### Examples

    df <- ORFik.template.experiment()
    design(df) # The 2 columns that decides the design here
    # If we subset it changes
    design(df[df$libtype == "RFP",])
    # Only single factor design, it picks first
    design(df, multi.factor = FALSE)

[Package ORFik version 1.14.7 Index]