Functions for creating and accessing the R-loop results (RL Results). These
are a type of object used for holding the results of the tests implemented
in RLSeq. They can be accessed using the rlresult function.
rlresult(object, resultName)RLRanges object.
Name of the result slot to access. See details.
The contents of the requested slot.
featureEnrichment
The tbl generated from running featureEnrich.
The structure and column descriptions are provided in detail within RLHub::feat_enrich_samples.
correlationMat
The matrix generated from running corrAnalyze.
Contains pairwise pearson correlations between all samples in RLBase and the supplied RLRanges object.
rlfsRes
The list generated from running analyzeRLFS.
See analyzeRLFS for description of structure.
noiseAnalysis
The tbl generated from running noiseAnalysis.
txFeatureOverlap
The tbl generated from running txFeatureOverlap.
geneAnnoRes
The tbl generated from running geneAnnotation.
predictRes
The list generated from running predictCondition.
rlRegionRes
The list generated from running rlRegionTest.
rlr <- readRDS(system.file("extdata", "rlrsmall.rds", package = "RLSeq"))
rlresult(rlr, "predictRes")
#> $Features
#> # A tibble: 12 × 3
#> feature raw_value processed_value
#> <chr> <dbl> <dbl>
#> 1 Z1 -0.989 3.78e+ 0
#> 2 Z2 -1.18 5.69e+ 1
#> 3 Zacf1 -0.972 4.49e- 3
#> 4 Zacf2 -1.28 5.14e+ 0
#> 5 ReW1 -0.513 4.32e+ 0
#> 6 ReW2 -1.18 7.79e+ 2
#> 7 ImW1 -2.73 -3.52e-15
#> 8 ImW2 1.04 2.09e+ 2
#> 9 ReWacf1 -1.20 1.80e+ 0
#> 10 ReWacf2 -1.25 5.80e+ 1
#> 11 ImWacf1 -0.582 2.71e-16
#> 12 ImWacf2 -1.26 4.42e+ 1
#>
#> $Criteria
#> $Criteria$`PVal Significant`
#> [1] TRUE
#>
#> $Criteria$`ZApex > 0`
#> [1] TRUE
#>
#> $Criteria$`ZApex > ZEdges`
#> [1] FALSE
#>
#> $Criteria$`Predicted 'POS'`
#> [1] FALSE
#>
#>
#> $prediction
#> [1] "NEG"
#>