Merge branch 'improve_assign_peptide_type_243' of https://github.com/…

…jpquast/protti into improve_assign_peptide_type_243
jpquast · Sep 24, 2024 · 008c498 · 008c498
2 parents b1c94c9 + cd31c1e
commit 008c498
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Showing 2 changed files with 6 additions and 11 deletions.
diff --git a/R/assign_peptide_type.R b/R/assign_peptide_type.R
@@ -50,11 +50,11 @@ peptide_type <- function(...) {
 #'
 #' @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", "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),
 #' )
 #'
 #' assign_peptide_type(data, aa_before, last_aa, aa_after, protein_id, start_pos)
@@ -72,35 +72,30 @@ assign_peptide_type <- function(data,
   peptide_data <- data %>%
     dplyr::distinct({{ aa_before }}, {{ last_aa }}, {{ aa_after }}, {{ protein_id }}, {{ start_pos }}, .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",
       TRUE,
       FALSE
     )) %>%
-
     # Determine C-terminal trypticity
     dplyr::mutate(C_term_tryp = dplyr::if_else(
       {{ last_aa }} == "K" | {{ last_aa }} == "R" | {{ aa_after }} == "",
       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",
       TRUE ~ "non-tryptic"
     )) %>%
-
     # Reassign semi-tryptic peptides at position 2 to fully-tryptic if no start_pos == 1
     dplyr::mutate(pep_type = dplyr::if_else(
       pep_type == "semi-tryptic" & {{ start_pos }} == 2 & !.data$has_start_pos_1 & C_term_tryp,
       "fully-tryptic",
       .data$pep_type
     )) %>%
-
     # Drop unnecessary columns
     dplyr::select(-N_term_tryp, -C_term_tryp, -has_start_pos_1)
 

diff --git a/tests/testthat/test-auxiliary_functions.R b/tests/testthat/test-auxiliary_functions.R
@@ -44,7 +44,7 @@ if (Sys.getenv("TEST_PROTTI") == "true") {
       expect_is(assigned_types, "data.frame")
       expect_equal(nrow(assigned_types), 6)
       expect_equal(ncol(assigned_types), 9)
-      expect_equal(assigned_types$pep_type, c("fully-tryptic", "semi-tryptic", "non-tryptic", "non-tryptic", "fully-tryptic","fully-tryptic"))
+      expect_equal(assigned_types$pep_type, c("fully-tryptic", "semi-tryptic", "non-tryptic", "non-tryptic", "fully-tryptic", "fully-tryptic"))
     })
 
     assigned_types <- data %>%