library(dplyr)
library(rlang)
library(tibble)
load("cpg_islands_indexes.rda")
all_sites <- readRDS("cpg_sites.RDS")
tumors <- sort(names(all_sites))
tumor <- "BRCA"
for (tumor in tumors){
hyper_sites <- all_sites[[tumor]] %>%
tibble::rownames_to_column("probe") %>%
dplyr::filter(type=="hyper" & n <= 10) %>%
dplyr::select(probe, index)
hypo_sites <- all_sites[[tumor]] %>%
tibble::rownames_to_column("probe") %>%
filter(type=="hypo" & n <= 10) %>%
select(probe, index)
sites <- list(hyper=set_names(hyper_sites$index, hyper_sites$probe),
hypo=set_names(hypo_sites$index, hypo_sites$probe))
assign(sprintf("%s_sites", tumor), sites)
assign(sprintf("%s_islands", tumor), cpg_islands_indexes[[tumor]])
}
usethis::use_data(overwrite=TRUE,
BLCA_sites,
BRCA_sites,
COAD_sites,
ESCA_sites,
HNSC_sites,
KIRC_sites,
KIRP_sites,
LIHC_sites,
LUAD_sites,
LUSC_sites,
PAAD_sites,
PRAD_sites,
THCA_sites,
UCEC_sites,
BLCA_islands,
BRCA_islands,
COAD_islands,
ESCA_islands,
HNSC_islands,
KIRC_islands,
KIRP_islands,
LIHC_islands,
LUAD_islands,
LUSC_islands,
PAAD_islands,
PRAD_islands,
THCA_islands,
UCEC_islands
)
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