R/get_NOTT2019_interactome.R
get_NOTT2019_interactome.RdOriginally from Nott et al. (2019). Specifically: aay0793-Nott-Table-S5.xlsx.
get_NOTT2019_interactome()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()
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()