plotGEEA: Scatterplots of enhancer activity~gene expression for max 16...
In BIMSBbioinfo/reg2gene: Predicting the target genes for regulatory elements

Description Usage Arguments Details Author(s) Examples

For GInteractions object that contains associations between a regulatory regions and TSSs (EP pairs),estimated association statistic,and corresponding p-values this function read files that contain quantified (and normalized) enhancer activity and gene expression levels for each data entry (cell type). Then this info is plotted as a scatterplot of enhancer activity~gene expression for max 16 EP pairs.

1 2	plotGEEA(enhPromPairs, indexTable, method = "H3K4me1", algorithm = "dcor", cohort = "Roadmap")

`enhPromPairs`	A GInteractions object of length 16 with the corresponding statistics as a results of either reg2gene modelling `associateReg2Gene`, meta-analysis `metaInteractions` or their pre-filtered versions `selectEP`. It requires information about statistics ("coef") and corresonding testing results ("pval"). In the future it could be adjusted for ("qval" or that it does not require any statistics).
`indexTable`	an output of the makeIndexTable() for given combination of methods/algorithms/cohorts; a table should contain the following columns: path - paths to .rds files; methods - a method type used for the analysis: eg. H3K4me1; algorithms - algorithm used for the analysis: eg. dcor, cohorts - cohort used for the analysis: eg. Roadmap; type - define whether results are produced by meta-analysis, from individual modelling or a result of regActivityAroundTSS() [NECESSARY]
`method`	"H3K4me1" (default; character). For which method to extract Enh~Promoter pairs. Common options: "H3K4me1","H3K27ac", "Methylation","DNase"
`algorithm`	"pearson" (default; character). For which algorithm to extract Enh~Promoter pairs. Common options:"pearson","spearman", "elasticnet","dcor","randomForest"
`cohort`	"Roadmap" (default; character). For which cohort to extract Enh~Promoter pairs. Common options:"Roadmap","Blueprint", "CEMT","McGill"

This function allows quick visualization of selected EP pairs as a scatterplot of corresponding levels of enhancer activity and gene expression for all data entries (cell types used in the modelling procedure: associateReg2Gene). This info is plotted for max 16 EP pairs, thus only the first 16 pairs will be plotted. It is useful in the case when one wants to visualize the background levels of enhancer activity and gene expression for TOP EP associations. Since, for each combination of cohort/methods/algorithms separated modelling is performed one needs to define a combination.

Inga Patarcic

require(ggplot2)
require(stringr)

## Not run: 

TOPgenes <- readRDS("/data/akalin/Projects/AAkalin_Catalog_RI/Results/Validation/Fishillevich/TOPgenesH3K4me1dcorRoadmap.rds")
IndexTable <- readRDS("/data/akalin/Projects/AAkalin_Catalog_RI/Results/Validation/Fishillevic/VoteD//CohortVoting_McGillH3K4me1.rds")

plotGEEA(TOPgenes,
       indexTable=IndexTable,
       method="H3K4me1",
       algorithm="dcor",
       cohort="Roadmap")


## End(Not run)