getConditions-function: Retrieve condition names from a targets data frame.
In ASpli: Analysis of Alternative Splicing Using RNA-Seq

Description Usage Arguments Value Author(s) See Also Examples

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.norm function.

1	getConditions( targets )

targets

A dataframe containing sample, bam and experimental factors columns

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

Estefania Mancini, Andres Rabinovich, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz

DUreport.norm, DUreport.offset

  
  # 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)