This function is a wrapper for calcExpectedPartitions that uses built-in partitions for a given reference genome assembly.

calcExpectedPartitionsRef(query, refAssembly, bpProportion = FALSE)

Arguments

query

A GenomicRanges or GenomicRangesList object with query regions

refAssembly

A character vector specifying the reference genome assembly (*e.g.* 'hg19'). This will be used to grab annotation models with getGeneModels, and chromosome sizes withgetChromSizes

bpProportion

logical indicating if overlaps should be calculated based on number of base pairs overlapping with each partition. bpProportion=FALSE does overlaps in priority order, bpProportion=TRUE counts number of overlapping base pairs between query and each partition.

Value

A data.frame indicating the number of query region overlaps in several genomic partitions.

Examples

calcExpectedPartitionsRef(vistaEnhancers, "hg19")
#> Warning: Chi-squared approximation may be incorrect
#>       partition observed   expected     log10OE Chi.square.pval
#> 1: promoterCore        5   0.801438  0.79510006         0.18400
#> 2: promoterProx       12  15.218192 -0.10318181         0.66900
#> 3:     threeUTR       12  16.693035 -0.14335406         0.48800
#> 4:      fiveUTR       11   4.461866  0.39187614         0.15800
#> 5:         exon       30  18.931636  0.19993312         0.14600
#> 6:       intron      441 510.750772 -0.06377044         0.00551
#> 7:   intergenic      828 772.143061  0.03033256         0.03060
#>                                                          method
#> 1: Pearson's Chi-squared test with Yates' continuity correction
#> 2: Pearson's Chi-squared test with Yates' continuity correction
#> 3: Pearson's Chi-squared test with Yates' continuity correction
#> 4: Pearson's Chi-squared test with Yates' continuity correction
#> 5: Pearson's Chi-squared test with Yates' continuity correction
#> 6: Pearson's Chi-squared test with Yates' continuity correction
#> 7: Pearson's Chi-squared test with Yates' continuity correction