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
applyOverlap            Apply function over counts
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
mdsChr22IntSpObj        Object of SummarizedExperiment type for intron
                        spanning reads 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
