In RajLabMSSM/echoannot: echoverse module: Annotate fine-mapping results

pkg <- read.dcf("../DESCRIPTION", fields = "Package")[1]
library(pkg, character.only = TRUE)

library(`r pkg`)

Nott2019

echoannot includes data generated by "Nott2019":

Nott A, Holtman IR, Coufal NG, ... Glass CK. Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. Science. 2019 Nov 29;366(6469):1134-1139. doi: 10.1126/science.aay0793. Epub 2019 Nov 14. PMID: 31727856; PMCID: PMC7028213.

Import data

superenhancers <- echoannot::get_NOTT2019_superenhancer_interactome()
enhancers_promoters <- echoannot::NOTT2019_get_promoter_interactome_data()
peaks <- echoannot::NOTT2019_get_epigenomic_peaks()

Plot

dat <- echodata::BST1
histo_out <- echoannot::NOTT2019_epigenomic_histograms(dat = dat)

In addition to the plot object, tables of both raw read ranges and called peaks are included in the output list.

knitr::kable(head(histo_out$data$raw))
knitr::kable(head(histo_out$data$peaks))

Corces2020

echoannot also includes data generated by "Corces2019":

Corces, M.R., Shcherbina, A., Kundu, S. et al. Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases. Nat Genet 52, 1158–1168 (2020). https://doi.org/10.1038/s41588-020-00721-x

Import data

bulkATACseq_peaks <- echoannot::get_CORCES2020_bulkATACseq_peaks()
cicero_coaccessibility <- echoannot::get_CORCES2020_cicero_coaccessibility()
hichip_fithichip_loop_calls <- echoannot::get_CORCES2020_hichip_fithichip_loop_calls()
scATACseq_celltype_peaks <- echoannot::get_CORCES2020_scATACseq_celltype_peaks()
scATACseq_peaks <- echoannot::get_CORCES2020_scATACseq_peaks()

Plot

peak_dat <- echoannot::granges_overlap(
    dat1 = dat,  
    chrom_col.1 = "CHR",
    start_col.1 = "POS",
    dat2 = scATACseq_celltype_peaks, 
    chrom_col.2 = "hg38_Chromosome",
    start_col.2 = "hg38_Start",
    end_col.2 = "hg38_Stop")
ggbio::autoplot(peak_dat, 
                ggplot2::aes(y=ExcitatoryNeurons, color=Effect))