Calculates the distribution of observed versus expected overlaps for a query set to a reference assembly — calcExpectedPartitionsRef • GenomicDistributions

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
#>          <char>    <int>      <num>       <num>           <num>
#> 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
#>                                                          <char>
#> 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