DEXSeqIntEREst          DEXSeq test for IntEREst object
IntEREst-package        IntEREst
InterestResult          Building SummarizedExperiment object from
                        results in IntEREst.
addAnnotation           Adding sample annotations to a
                        'SummarizedExperiment' object
annotateU12             Annotate the U12 (and U2) type introns
attributes              Extracting values of useful attributes of
                        SummarizedExperiment objects
boxplot-method          boxplot - method
buildSsTypePwms         Building Position Weight Matrices for Splice
                        Sites of U12 and U2 type introns.
counts-method           Counts - method
deseqInterest           DESeq2 analysis for IntEREst object
exactTestInterest       Exact test
getRepeatTable          Get table of regions with repetetive DNA
                        sequences
glmInterest             generalized linear model likelihood ratio tests
interest                Wrapper function: Parallel run
interest.sequential     Wrapup function: Sequential running
interestResultIntEx     Building results object that contains
                        Intron-retention and exon-exon junction
                        information
intexIndex              Extract index of intron or exon rows
lfc                     Log fold change
mdsChr22ExObj           Object of SummarizedExperiment type for
                        exon-exon junction of MDS data
mdsChr22Obj             Object of SummarizedExperiment type for intron
                        retention MDS data
mergeInterestResult     merge two SummarizedExperiment objects into one
plot-method             plot - method
psi                     Psi values estimation
pwmU12db                PWM of U12 and U2-type introns splice sites
qlfInterest             quasi-likelihood F-test
readInterestResults     Read interest/interest.sequential results text
                        files
referencePrepare        Creates reference file
subInterestResult       Extract subset of object
treatInterest           Differential retention test relative to a
                        threshold
u12                     U12 data
u12Boxplot              U12 boxplot
u12BoxplotNb            boxplot U12 introns retention levels (or
                        flanking exons junction levels) and
                        (up/down)stream U2 introns (or exons junction
                        levels)
u12DensityPlot          Density plot of fld changes of intron retention
                        and exon-exon junction levels
u12Index                Extract index of U12 introns rows
u12NbIndex              Extract index of U2 introns (up/down)stream of
                        U12 introns rows
unionRefTr              Union introns/exons of transcripts
updateRowDataCol        Updating contents of 'rowData' of
                        'SummarizedExperiment' objects
