get_NOTT2019_interactome: Brain cell type-specific enhancers, promoters, and...

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

Brain cell type-specific enhancers, promoters, and interactomes

Description

Originally from Nott et al. (2019). Specifically: aay0793-Nott-Table-S5.xlsx.

Usage

get_NOTT2019_interactome()

Source

https://doi.org/10.1126/science.aay0793

file <- file.path( "~/Desktop/Fine_Mapping/echolocatoR/annotations", "NOTT2019/aay0793-Nott-Table-S5.xlsx" ) sheets <- readxl::excel_sheets(file) enh_prom_sheets <- grep("enhancers|promoters", sheets, value = TRUE) other_sheets <- grep("enhancers|promoters", sheets, value = TRUE, invert = TRUE ) NOTT2019_interactome <- lapply(other_sheets, function(s) { readxl::read_excel(file, sheet = s, skip = 2) }) NOTT2019_interactome <- append( NOTT2019_interactome, lapply(enh_prom_sheets, function(s) { readxl::read_excel(file, sheet = s, skip = 2, col_names = c("chr", "start", "end") ) }) ) names(NOTT2019_interactome) <- c(other_sheets, enh_prom_sheets) #### piggyback #### tmp <- file.path(tempdir(), "NOTT2019_interactome.rds") saveRDS(NOTT2019_interactome, tmp) piggyback::pb_upload( file = tmp, repo = "RajLabMSSM/echoannot" )

NOTT2019_interactome <- get_NOTT2019_interactome()

See Also

Other NOTT2019: NOTT2019_bigwig_metadata, NOTT2019_epigenomic_histograms(), NOTT2019_get_epigenomic_peaks(), NOTT2019_get_interactions(), NOTT2019_get_interactome(), NOTT2019_get_promoter_celltypes(), NOTT2019_get_promoter_interactome_data(), NOTT2019_get_regulatory_regions(), NOTT2019_plac_seq_plot(), NOTT2019_superenhancers(), get_NOTT2019_superenhancer_interactome()

RajLabMSSM/echoannot documentation built on Oct. 26, 2023, 2:41 p.m.