Fixing assign_peptide_type

R/assign_peptide_type.R

@@ -24,7 +24,9 @@ peptide_type <- function(...) {
 #' peptide is located at the N- or C-terminus of a protein and fulfills the criterium to be
 #' fully-tryptic otherwise, it is also considered as fully-tryptic. Peptides that only fulfill the
 #' criterium on one terminus are semi-tryptic peptides. Lastly, peptides that are not fulfilling
-#' the criteria for both termini are non-tryptic peptides.
+#' the criteria for both termini are non-tryptic peptides. In addition, peptides that miss the initial
+#' Methionine of a protein are considered "tryptic" at that site if there is no other peptide
+#' starting at position 1 for that protein.
 #'
 #' @param data a data frame containing at least information about the preceding and C-terminal
 #' amino acids of peptides.
@@ -36,80 +38,86 @@ peptide_type <- function(...) {
 #' acid as one letter code.
 #' @param protein_id a character column in the \code{data} data frame that contains the protein
 #' accession numbers.
-#' @param start_pos A numeric column in the \code{data} data frame that contains the start position of
-#' each peptide within the corresponding protein. This is used to check if the peptide starts at position 1
-#' or position 2, which affects whether the peptide can be considered fully-tryptic.
-#'
+#' @param start a numeric column in the \code{data} data frame that contains the start position of
+#' each peptide within the corresponding protein. This is used to check if the protein is consistently
+#' missing the initial Methionine, making peptides starting at position 2 "tryptic" on that site.
 #'
 #' @return A data frame that contains the input data and an additional column with the peptide
 #' type information.
 #' @import dplyr
 #' @importFrom magrittr %>%
 #' @importFrom rlang .data
+#' @importFrom stringr str_detect
 #' @export
 #'
 #' @examples
 #' data <- data.frame(
-#'   aa_before = c("K", "S", "K", "S", "T", "M"),
-#'   last_aa = c("R", "K", "R", "K", "Y", "K"),
-#'   aa_after = c("T", "R", "T", "R", "T", "R"),
-#'   protein_id = c("P1", "P1", "P3", "P3", "P2", "P2"),
-#'   start_pos = c(2, 2, 1, 2, 1, 2),
-#' )
+#'   aa_before = c("K", "M", "", "M", "S", "M", "-"),
+#'   last_aa = c("R", "K", "R", "R", "Y", "K", "K"),
+#'   aa_after = c("T", "R", "T", "R", "T", "R", "T"),
+#'   protein_id = c("P1", "P1", "P3", "P3", "P2", "P2", "P2"),
+#'   start = c(38, 2, 1, 2, 10, 2, 1)
+#'   )
 #'
-#' assign_peptide_type(data, aa_before, last_aa, aa_after, protein_id, start_pos)
+#' assign_peptide_type(data, aa_before, last_aa, aa_after, protein_id, start)
 assign_peptide_type <- function(data,
                                 aa_before = aa_before,
                                 last_aa = last_aa,
                                 aa_after = aa_after,
                                 protein_id = protein_id,
-                                start_pos = start_pos) {
+                                start = start) {
   # Check if there's any peptide starting at position 1 for each protein
   start_summary <- data %>%
     dplyr::group_by({{ protein_id }}) %>%
-    dplyr::summarize(has_start_pos_1 = any({{ start_pos }} == 1), .groups = "drop")
+    dplyr::summarize(has_start_1 = any({{ start }} == 1), .groups = "drop")
 
   peptide_data <- data %>%
-    dplyr::distinct({{ aa_before }}, {{ last_aa }}, {{ aa_after }}, {{ protein_id }}, {{ start_pos }}, .keep_all = TRUE) %>%
+    dplyr::distinct({{ aa_before }}, {{ last_aa }}, {{ aa_after }}, {{ protein_id }}, {{ start }}, .keep_all = TRUE) %>%
     dplyr::left_join(start_summary, by = rlang::as_name(rlang::enquo(protein_id))) %>%
     # Determine N-terminal trypticity
     dplyr::mutate(N_term_tryp = dplyr::if_else(
-      {{ aa_before }} == "" | {{ aa_before }} == "K" | {{ aa_before }} == "R",
+      !stringr::str_detect({{ aa_before }}, "[A-Y]") | {{ aa_before }} == "K" | {{ aa_before }} == "R",
       TRUE,
       FALSE
     )) %>%
     # Determine C-terminal trypticity
     dplyr::mutate(C_term_tryp = dplyr::if_else(
-      {{ last_aa }} == "K" | {{ last_aa }} == "R" | {{ aa_after }} == "",
+      {{ last_aa }} == "K" | {{ last_aa }} == "R" | !stringr::str_detect({{ aa_after }}, "[A-Y]"),
       TRUE,
       FALSE
     )) %>%
     # Assign peptide type based on N-term and C-term trypticity
     dplyr::mutate(pep_type = dplyr::case_when(
-      N_term_tryp & C_term_tryp ~ "fully-tryptic",
-      N_term_tryp | C_term_tryp ~ "semi-tryptic",
+      .data$N_term_tryp & .data$C_term_tryp ~ "fully-tryptic",
+      .data$N_term_tryp | .data$C_term_tryp ~ "semi-tryptic",
       TRUE ~ "non-tryptic"
     )) %>%
-    # Reassign semi-tryptic peptides at position 2 to fully-tryptic if no start_pos == 1
+    # Reassign semi-tryptic peptides at position 2 to fully-tryptic if no start == 1
+    dplyr::mutate(pep_type = dplyr::if_else(
+      pep_type == "semi-tryptic" & {{ start }} == 2 & !.data$has_start_1 & .data$C_term_tryp,
+      "fully-tryptic",
+      .data$pep_type
+    )) %>%
+    # Reassign non-tryptic peptides at position 2 to semi-tryptic if no start == 1
     dplyr::mutate(pep_type = dplyr::if_else(
-      pep_type == "semi-tryptic" & {{ start_pos }} == 2 & !.data$has_start_pos_1 & C_term_tryp,
+      pep_type == "non-tryptic" & {{ start }} == 2 & !.data$has_start_1 & !.data$C_term_tryp,
       "fully-tryptic",
       .data$pep_type
     )) %>%
     # Drop unnecessary columns
-    dplyr::select(-N_term_tryp, -C_term_tryp, -has_start_pos_1)
+    dplyr::select(-c("N_term_tryp", "C_term_tryp", "has_start_1"))
 
   # Join back to original data to return the full result
   result <- data %>%
     dplyr::left_join(
       peptide_data %>%
-        dplyr::select({{ aa_before }}, {{ last_aa }}, {{ aa_after }}, {{ protein_id }}, {{ start_pos }}, pep_type),
+        dplyr::select({{ aa_before }}, {{ last_aa }}, {{ aa_after }}, {{ protein_id }}, {{ start }}, .data$pep_type),
       by = c(
         rlang::as_name(rlang::enquo(aa_before)),
         rlang::as_name(rlang::enquo(last_aa)),
         rlang::as_name(rlang::enquo(aa_after)),
         rlang::as_name(rlang::enquo(protein_id)),
-        rlang::as_name(rlang::enquo(start_pos))
+        rlang::as_name(rlang::enquo(start))
       )
     )