getConditions {ASpli} | R Documentation

## Retrieve condition names from a targets data frame.

### Description

Targets data frame contains experimental factors values for each sample. This function generates a simple name for each unique condition resulting from the combination of all experimental factors. The order of the conditions given by `getConditions` is the same that in `contrast` argument of `DUreport` function.

### Usage

      getConditions( targets )

### Arguments

`targets` | A dataframe containing sample, bam and experimental factors columns

### Value

A character vector with the names of the conditions derived from experimental factors.

### Author(s)

Estefania Mancini, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz

### See Also

`DUreport`,

### Examples

      # Define bam files, sample names and experimental factors for targets.
      bamFileNames <- c( "A_C_0.bam", "A_C_1.bam", "A_C_2.bam",
                         "A_D_0.bam", "A_D_1.bam", "A_D_2.bam" )
      targets <- data.frame(
                   row.names = paste0('Sample_',c(1:6)),
                   bam = system.file( 'extdata', bamFileNames, package="ASpli" ),
                   factor1 = c( 'C','C','C','D','D','D') )

      # Load reads from bam files.
      # Return value is c('C', 'D') in this example.
      conditions <- getConditions(targets)

      # Define bam files, sample names and experimental factors for targets.
      bamFileNames <- c( "A_C_0.bam", "A_C_1.bam", "A_C_2.bam", "A_C_3.bam",
                         "A_D_0.bam", "A_D_1.bam", "A_D_2.bam", "A_D_3.bam"  )
      targets <- data.frame(
                   row.names = paste0('Sample_',c(1:8)),
                   bam = file.path( 'extdata', bamFileNames, package="ASpli" ),
                   factor1 = c( 'C','C','C','C','D','D','D','D'),
                   factor2 = c( 'E','E','F','F','E','E','F','F')  )

      # Load reads from bam files.
      # Return value is c("C_E", "C_F", "D_E", "D_F") in this example.
      conditions <- getConditions(targets)

[Package ASpli version 1.10.0 Index]