# BiologicalReplicate class.
setClass( "BiologicalReplicate", slots = c( assay_names = "vector", technical_replicate_id = "character" ) )
##############################
# BiologicalReplicate Generics
# assay_names getter.
setGeneric( "biorep_assay_names", function( object ) standardGeneric( "biorep_assay_names" ) )
# technical_replicate_id getter.
setGeneric( "technical_replicate_id", function( object ) standardGeneric( "technical_replicate_id" ) )
#############################
# BiologicalReplicate Methods
# Constructor.
setMethod( "initialize", "BiologicalReplicate", function( .Object, assayNames, techRepId = NULL ) {
# Make sure that there's only one technical replicate ID.
if( length( techRepId ) > 1 ) {
cat( "ERROR - These do not look like technical replicate IDs:\n" )
print( techRepId )
cat( "ERROR - Please check technical replicate IDs in XML config.\n" )
stop( "ERROR - Problem with technical replicate IDs. Cannot continue." )
}
.Object@assay_names <- make.names( assayNames )
if( !is.null( techRepId ) ) {
.Object@technical_replicate_id <- techRepId
}
return( .Object )
})
# Method for assay_names getter.
setMethod( "biorep_assay_names", "BiologicalReplicate", function( object ) object@assay_names )
# Method for technical_replicate_id getter.
setMethod( "technical_replicate_id", "BiologicalReplicate", function( object ) object@technical_replicate_id )
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