`R/partition-plots.R`

`calcExpectedPartitionsRef.Rd`

This function is a wrapper for `calcExpectedPartitions`

that uses
built-in partitions for a given reference genome assembly.

`calcExpectedPartitionsRef(query, refAssembly, bpProportion = FALSE)`

- 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 with`getChromSizes`

- 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.

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

```
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
```