Filter annotations

Description

This function filters initial annotations.

Usage

filter_annotations(
  annotations = get_params(step =
    "filter_annotations")\$files\$annotations\$prepared\$structural,
  features = get_params(step = "filter_annotations")\$files\$features\$prepared,
  rts = get_params(step = "filter_annotations")\$files\$libraries\$temporal\$prepared,
  output = get_params(step = "filter_annotations")\$files\$annotations\$filtered,
  tolerance_rt = get_params(step = "filter_annotations")\$ms\$tolerances\$rt\$library
)

Arguments

annotations	Prepared annotations file
features	Prepared features file
rts	Prepared retention time library
output	Output file
tolerance_rt	Tolerance to filter retention time

Value

The path to the filtered annotations

Examples

library("tima")

copy_backbone()
go_to_cache()
github <- "https://raw.githubusercontent.com/"
repo <- "taxonomicallyinformedannotation/tima-example-files/main/"
dir <- paste0(github, repo)
annotations <- get_params(step = "filter_annotations")$files$annotations$prepared$structural[[2]] |>
  gsub(
    pattern = ".gz",
    replacement = "",
    fixed = TRUE
  )
features <- get_params(step = "filter_annotations")$files$features$prepared |>
  gsub(
    pattern = ".gz",
    replacement = "",
    fixed = TRUE
  )
rts <- get_params(step = "filter_annotations")$files$libraries$temporal$prepared |>
  gsub(
    pattern = ".gz",
    replacement = "",
    fixed = TRUE
  )
get_file(url = paste0(dir, annotations), export = annotations)
get_file(url = paste0(dir, features), export = features)
get_file(url = paste0(dir, rts), export = rts)
filter_annotations(
  annotations = annotations,
  features = features,
  rts = rts
)
unlink("data", recursive = TRUE)