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)Filter annotations
Description
This function filters initial annotations by removing MS1-only annotations that also have spectral matches, and optionally filtering by retention time tolerance when RT libraries are available.
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
|
Character vector or list of paths to prepared annotation files |
features
|
Character string path to prepared features file. Must contain a feature_id column. The rt column is optional; if absent, RT filtering is skipped even when an RT library is provided.
|
rts
|
Character string path to prepared retention time library (optional) |
output
|
Character string path for filtered annotations output |
tolerance_rt
|
Numeric RT tolerance in minutes for library matching |
Value
Character string path to the filtered annotations file