`R/partition-plots.R`

`calcExpectedPartitions.Rd`

Calculates expected partiton overlap based on contribution of each feature (partition) to genome size. Expected and observed overlaps are then compared.

```
calcExpectedPartitions(
query,
partitionList,
genomeSize = NULL,
remainder = "intergenic",
bpProportion = FALSE
)
```

- query
GRanges or GRangesList with regions to classify.

- partitionList
An ORDERED (if bpProportion=FALSE) and NAMED list of genomic partitions GRanges. This list must be in priority order; the input will be assigned to the first partition it overlaps. However, if bpProportion=TRUE, the list does not need ordering.

- genomeSize
The number of bases in the query genome. In other words, the sum of all chromosome sizes.

- remainder
Which partition do you want to account for 'everything else'?

- 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 assigning each element of a GRanges object to a partition from a previously provided partitionList.The data.frame also contains Chi-square p-values calculated for observed/expected overlaps on each individual partition.

```
partitionList = genomePartitionList(geneModels_hg19$genesGR,
geneModels_hg19$exonsGR,
geneModels_hg19$threeUTRGR,
geneModels_hg19$fiveUTRGR)
chromSizes = getChromSizes('hg19')
genomeSize = sum(chromSizes)
calcExpectedPartitions(vistaEnhancers, partitionList, genomeSize)
#> 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
```