coverageByTranscriptFST: Get coverage from fst large coverage format

In JokingHero/ORFik: Open Reading Frames in Genomics

Get coverage from fst large coverage format

Description

Get coverage from fst large coverage format

Usage

coverageByTranscriptFST(grl, fst_index, columns = NULL)

Arguments

grl	a GRangesList
fst_index	a path to an existing fst index file
columns	NULL or character, default NULL. Else must be a subset of names in the fst files. Run ids etc.

Value

a list, each element is a data.table of coverage

Examples

library(data.table)
library(ORFik)
grl <- GRangesList("1:1-5:+")
tempdir <- tempdir()
fst_index <- file.path(tempdir, "coverage_index.fst")
mock_run_names <- c("SRR1010101", "SRR1010102", "SRR1010103")
coverage_file <- file.path(tempdir, paste0("coverage_1_part1_",
 c("forward", "reverse"), ".fst"))
mock_coverage <- setnames(setDT(lapply(mock_run_names, function(x) {
 sample(seq(0, 100), 100, replace = TRUE, prob = c(0.95, rep(0.01, 100)))})),
 mock_run_names)
mock_index <- data.table(chr = "1", start = 1, end = nrow(mock_coverage),
 file_forward = coverage_file[1], file_reverse = coverage_file[2])

fst::write_fst(mock_index, fst_index)
fst::write_fst(mock_coverage, coverage_file[1])

coverageByTranscriptFST(grl, fst_index)
coverageByTranscriptFST(grl, fst_index, c("SRR1010101", "SRR1010102"))

JokingHero/ORFik documentation built on June 9, 2025, 8:46 p.m.