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| 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 |
| 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 |