Man pages for IntEREst
Intron-Exon Retention Estimator

addAnnotationAdding sample annotations to a 'SummarizedExperiment' object
annotateU12Annotate the U12 (and U2) type introns
applyOverlapApply function over counts
attributesExtracting values of useful attributes of...
boxplot-methodboxplot - method
buildSsTypePwmsBuilding Position Weight Matrices for Splice Sites of U12 and...
counts-methodCounts - method
deseqInterestDESeq2 analysis for IntEREst object
DEXSeqIntEREstDEXSeq test for IntEREst object
exactTestInterestExact test
getRepeatTableGet table of regions with repetetive DNA sequences
glmInterestgeneralized linear model likelihood ratio tests
interestWrapper function: Parallel run
interestResultBuilding SummarizedExperiment object from results in...
interestResultIntExBuilding results object that contains Intron-retention and...
interest.sequentialWrapup function: Sequential running
intexIndexExtract index of intron or exon rows
lfcLog fold change
mdsChr22ExObjObject of SummarizedExperiment type for exon-exon junction of...
mdsChr22IntSpObjObject of SummarizedExperiment type for intron spanning reads...
mdsChr22ObjObject of SummarizedExperiment type for intron retention MDS...
mergeInterestResultmerge two SummarizedExperiment objects into one
plot-methodplot - method
psiPsi values estimation
pwmU12dbPWM of U12 and U2-type introns splice sites
qlfInterestquasi-likelihood F-test
readInterestResultsRead interest/interest.sequential results text files
referencePrepareCreates reference file
subInterestResultExtract subset of object
treatInterestDifferential retention test relative to a threshold
u12U12 data
u12BoxplotU12 boxplot
u12BoxplotNbboxplot U12 introns retention levels (or flanking exons...
u12DensityPlotDensity plot of fld changes of intron retention and exon-exon...
u12IndexExtract index of U12 introns rows
u12NbIndexExtract index of U2 introns (up/down)stream of U12 introns...
unionRefTrUnion introns/exons of transcripts
updateRowDataColUpdating contents of 'rowData' of 'SummarizedExperiment'...
IntEREst documentation built on Nov. 8, 2020, 8:05 p.m.