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]