Intron-Exon Retention Estimator

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Documentation for package ‘IntEREst’ version 1.28.0

• 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
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
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