#' @title Filter annotations
#'
#' @description This function filters initial annotations.
#'
#' @param annotations Prepared annotations file
#' @param features Prepared features file
#' @param rts Prepared retention time library
#' @param output Output file
#' @param tolerance_rt Tolerance to filter retention time
#'
#' @return NULL
#'
#' @export
#'
#' @examples NULL
filter_annotations <-
function(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$rt$minutes) {
stopifnot(
"Annotations file(s) do(es) not exist" = all(lapply(X = annotations, FUN = file.exists) |> unlist())
)
stopifnot(
"Retention time file(s) do(es) not exist" = all(lapply(X = rts, FUN = file.exists) |> unlist())
)
stopifnot("Your features file does not exist." = file.exists(features))
if (length(rts) == 0) {
rts <- NULL
}
log_debug(x = "... features")
features_table <- tidytable::fread(
file = features,
colClasses = "character",
na.strings = c("", "NA")
)
log_debug(x = "... annotations")
annotation_table <- lapply(
X = annotations,
FUN = tidytable::fread,
na.strings = c("", "NA"),
colClasses = "character"
) |>
tidytable::bind_rows()
log_debug(x = "... retention times")
if (!is.null(rts)) {
rt_table <- lapply(
X = rts,
FUN = tidytable::fread,
na.strings = c("", "NA"),
colClasses = "character"
) |>
tidytable::bind_rows() |>
tidytable::rename(rt_target = rt)
}
features_annotated_table_1 <- features_table |>
tidytable::left_join(annotation_table)
if (!is.null(rts)) {
log_debug(
"Filtering annotations outside of",
tolerance_rt * 3,
"minutes tolerance"
)
features_annotated_table_2 <- features_annotated_table_1 |>
tidytable::left_join(rt_table) |>
tidytable::mutate(
candidate_structure_error_rt = as.numeric(rt) -
as.numeric(rt_target)
) |>
tidytable::arrange(abs(candidate_structure_error_rt)) |>
tidytable::distinct(-candidate_structure_error_rt, -rt_target,
.keep_all = TRUE
) |>
## ISSUE see #149 adapt for types and improve the * 3
tidytable::filter(abs(candidate_structure_error_rt) <= abs(tolerance_rt * 3) | is.na(candidate_structure_error_rt)) |>
tidytable::select(-rt_target, -type)
} else {
log_debug("No RT library provided, not filtering anything")
features_annotated_table_2 <- features_annotated_table_1 |>
tidytable::mutate(candidate_structure_error_rt = NA)
}
log_debug(
crayon::green(
nrow(features_annotated_table_1) - nrow(features_annotated_table_2)
),
"Candidates were removed based on retention time."
)
## in case some features had a single filtered annotation
final_table <- features_table |>
tidytable::left_join(features_annotated_table_2)
rm(
features_table,
annotation_table,
features_annotated_table_1,
features_annotated_table_2
)
export_params(
parameters = get_params(step = "filter_annotations"),
step = "filter_annotations"
)
export_output(
x = final_table,
file = output[[1]]
)
rm(final_table)
return(output[[1]])
}
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