library(rtracklayer)
library(stringr)
library(data.table)
library(dplyr)
files = list.files('./', full.names=TRUE, pattern='bedGraph')
lcov = list()
for(i in 1:length(files)){
file = files[i]
name = basename(file)
name = str_replace(name,'\\..+','')
print(name)
f = fread(file) %>%
filter(V4 > 0.25) %>%
mutate(V4 = round(V4,2)) %>%
as.data.frame()
g = with(f, GRanges(V1, IRanges(V2+1,V3), weight=V4))
cov = coverage(g, weight=as.integer(g$weight*100))
lcov[[name]] = cov
}
lcov = Reduce(c, lcov)
saveRDS(lcov, 'hg19.phastCons46way.placental.RleList.rds')
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