Produces a boxplot for the asymmetry coefficients for each row in the input matrix. Normal observations are simulated using the observed sample means and variances, and their asymmetry coefficients are added to the plot.
Estimate expression of gene splicing variants, assuming that the set of variants is known. When rpkm is set to TRUE, fragments per kilobase per million are returned. Otherwise relative expression estimates are returned.
Obtains expression estimates from denovoGenomeExpr objects, as returned by calcDenovo. When rpkm is set to TRUE, fragments per kilobase per million are returned. Otherwise relative expression estimates are returned.
denovoGeneExpr stores inferred expression for de novo splicing variants for a single gene. denovoGenomeExpr stores the information for several genes (typically, the whole genome).
denovoGeneExpr stores inferred expression for de novo splicing variants for a single gene. denovoGenomeExpr stores the information for several genes (typically, the whole genome).
Compute fragment start distributions by using reads aligned to genes with only one annotated variant. Estimate fragment length distribution using fragments aligned to long exons (>1000nt). Fragment length is defined as the distance between the start of the left-end read and the end of the right-end read.
annotatedGenome objects store information regarding genes and transcripts. When there's an overlap in exons between several genes, these genes are grouped into gene islands. getIsland retrieves the island to which each gene or transcript was assigned, while getChr indicates the chromosome.
providing 
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