Intron-Exon Retention Estimator


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Documentation for package ‘IntEREst’ version 1.28.0

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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