# Intron-Exon Retention Estimator

## Documentation for package ‘IntEREst’ version 1.4.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

IntEREst-package | 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
counts.InterestResults | Counts - method
deseqInterest | DESeq2 analysis for IntEREst object
DEXSeqIntEREst | DEXSeq test for IntEREst object
exactTestInterest | Exact test
getAnnotation | Extracting values of useful attributes of SummarizedExperiment objects
getRepeatTable | Get table of regions with repetetive DNA sequences
glmInterest | generalized linear model likelihood ratio tests
IntEREst | IntEREst
interest | Wrapper function: Parallel run
interest.sequential | Wrapup function: Sequential running
InterestResult | Building SummarizedExperiment object from results in IntEREst.
interestResultIntEx | Building results object that contains Intron-retention and exon-exon junction information
intexBoxplot | boxplot - method
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
plot.InterestResult | 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
scaledRetention | Extracting values of useful attributes of SummarizedExperiment objects
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
u12DensityPlotIntron | 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