Man pages for IntEREst
Intron-Exon Retention Estimator

addAnnotationAdding sample annotations to a 'SummarizedExperiment' object
annotateU12Annotate the U12 (and U2) type introns
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
eBayesInterestLimma based statistical test
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
mdsChr22ObjObject of SummarizedExperiment type for MDS data
mergeInterestResultmerge two SummarizedExperiment objects into one
plot-methodplot - method
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. 17, 2017, 10:51 a.m.