The main class in Rcade. This class contains data pertaining to any relevant DE experiments, ChIP-seq experiments, and Rcade output from linking the previous two.
● Data Source:
BioConductor
● Keywords: misc
● Alias: Rcade-class
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The main function in Rcade - reads in DE information, processes ChIP data from raw .bam files, and then combines the two to form an Rcade object.
● Data Source:
BioConductor
● Keywords: misc
● Alias: RcadeAnalysis
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Class for storing information pertaining to a set of ChIP-seq experiments - in particular, count data and
● Data Source:
BioConductor
● Keywords: misc
● Alias: RcadeTrack-class
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Most Rcade users will not need to call this function directly. This function constructs a full Rcade table from ChIP and DE data.
● Data Source:
BioConductor
● Keywords: ~kwd1, ~kwd2
● Alias: constructRcadeTable
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Most Rcade users will not need to call this function directly. Given targets information linking to bam files, count the reads that lie in defined bins.
● Data Source:
BioConductor
● Keywords:
● Alias: countReads
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Defines bins about the 5' end of certain features of interest - these features are usually transcripts.
● Data Source:
BioConductor
● Keywords:
● Alias: defineBins
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Most Rcade users will not need to call this function directly. A function that provides a wrapper for the methods in the BaySeq package.
● Data Source:
BioConductor
● Keywords: ~kwd1, ~kwd2
● Alias: diffCountsBaySeq
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Methods for exporting Rcade objects, either to disk or in R.
● Data Source:
BioConductor
● Keywords: methods
● Alias: exportRcade, exportRcade,Rcade-method, exportRcade-methods
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providing 
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