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 |