fix bugs

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: metid
 Title: Metabolite identification based on MS1 and MS2 spectra
-Version: 1.2.32
+Version: 1.2.33
 Date: 2024-09-10
 Authors@R: c(
     person(given = "Xiaotao",

NEWS.md

@@ -183,3 +183,7 @@
 
 * Add more functions for more efficient annotation.
 
+# Version 1.2.33 (2024-09-10)
+
+* Fix bugs.
+

R/52_check_parameters_functions.R

@@ -1,5 +1,6 @@
 
 
+
 #' Validate Parameters for Metabolite Annotation
 #'
 #' This function validates the input parameters required for the metabolite annotation process. It checks the `mass_dataset` object, the annotation database, the adduct table, and various matching and weighting parameters to ensure they are correctly specified.
@@ -303,11 +304,6 @@ check_database <-
     ##check MS2 information
     ####if based_on has ms2, the object and database should have ms2 information
     if ("ms2" %in% based_on) {
-      ##check if object have ms2 information
-      if (length(object@ms2_data) == 0) {
-        stop("The object should have MS2 information.\n")
-      }
-
       ##Check if database have MS2 spectra or not
       spectra_pos_number <-
         database@spectra.data[['Spectra.positive']] %>%
@@ -461,11 +457,11 @@ check_adduct_table <-
 #'
 #' # Example MS2 info
 #' ms2_info <- list(
-#'   spectrum1 = matrix(c(75, 1000, 80, 2000), 
-#'   ncol = 2, byrow = TRUE, 
+#'   spectrum1 = matrix(c(75, 1000, 80, 2000),
+#'   ncol = 2, byrow = TRUE,
 #'   dimnames = list(NULL, c("mz", "intensity"))),
-#'   spectrum2 = matrix(c(85, 3000, 90, 1500), 
-#'   ncol = 2, byrow = TRUE, 
+#'   spectrum2 = matrix(c(85, 3000, 90, 1500),
+#'   ncol = 2, byrow = TRUE,
 #'   dimnames = list(NULL, c("mz", "intensity")))
 #' )
 #'

_pkgdown.yml

@@ -22,90 +22,6 @@ template:
     bootswatch: flatly
     ganalytics: UA-000000-01
 
-reference:
-  - title: Database construction
-    desc: Construct in-house or public MS2 spectra database.
-    contents:
-    - construct_database
-    - correct_database_rt
-    - get_ms2_spectrum
-    - construct_massbank_database
-    - construct_mona_database
-    - filter_adducts
-
-  - title: Metabolite identification
-    desc: Metabolite identification based on MS1 and MS2 databases.
-    contents:
-    - which_has_identification
-    - trans_to_new_style
-    - ms2plot
-    - identify_single_peak
-    - identify_metabolites_params
-    - identify_metabolites
-    - get_parameters
-    - get_ms2_spectrum_from_object
-    - get_identification_table
-    - get_identification_table_all
-    - get_iden_info
-    - filter_identification
-    - annotate_metabolites_mass_dataset
-    - annotate_single_peak_mass_dataset
-    - getIdentificationTable2
-    - getMS2spectrum
-    - get_parameters_metid
-    - identify_metabolite_all
-    - identify_ms2_only
-    - identify_peak
-    - metIdentify
-    - metIdentify_mass_dataset
-    - ms2_plot_mass_dataset
-    - mzIdentify
-    - mzIdentifyParam
-    - mzIdentify_mass_dataset
-    - mzIdentify_mass_dataset2
-
-  - title: Data
-    desc: Some data embed in metid
-    contents:
-    - hilic.pos
-    - hilic.neg
-    - rp.pos
-    - rp.neg
-    - msDatabase_hilic0.0.2
-    - msDatabase_rplc0.0.2
-    - orbitrap_database0.0.3
-    - snyder_database_hilic0.0.3
-    - snyder_database_rplc0.0.3
-
-  - title: Other functions
-    desc: Other usefull functions in metid
-    contents:
-    - readMGF
-    - readMSP
-    - readMZXML
-    - metid
-    - metid_conflicts
-    - metid_logo
-    - metid_packages
-    - readMSP_MoNA
-    - read_mgf_experiment
-    - read_mgf_gnps
-    - read_mgf_mona
-    - read_msp
-    - read_msp_database
-    - read_msp_gnps
-    - read_msp_mona
-    - colnames.databaseClass
-    - summary_annotation_table
-    - databaseClass-class
-    - metIdentifyClass-class
-    - write_mgf_gnps
-    - write_mgf_massbank
-    - write_mgf_mona
-    - write_msp_gnps
-    - write_msp_massbank
-    - write_msp_mona
-
 navbar:
   title: "sparklyr" 
   # type: inverse
@@ -132,7 +48,15 @@ navbar:
       - text: Correct retention times in database according to internal standards
         href: articles/rt_correction.html
       - text: -------
-      - text: "Metabolite identification"
+      - text: "metid for mass_dataset class object"
+      - text: "Annotate metabolites"
+        href: articles/work_with_mass_dataset.html
+      - text: "Annotate single peak"
+        href: articles/annotate_single_peak_mass_dataset.html
+      - text: "MS2 plot"
+        href: articles/ms2_plot_mass_dataset.html
+      - text: -------
+      - text: "Old pipeline"
       - text: Metabolite identification using MS1 database
         href: articles/metabolite_annotation_using_MS1.html
       - text: Metabolite identification using MS2 database
@@ -145,14 +69,6 @@ navbar:
       - text: "Others"
       - text: Other usefull tools
         href: articles/other_tools.html
-      - text: -------
-      - text: "metid for mass_dataset class object"
-      - text: "Work with mass_dataset class object"
-        href: articles/work_with_mass_dataset.html
-      - text: "Annotate single peak in mass_dataset"
-        href: articles/annotate_single_peak_mass_dataset.html
-      - text: "MS2 plot in mass_dataset"
-        href: articles/ms2_plot_mass_dataset.html
     twitter:
       icon: "fab fa-twitter fa-lg"
       href: https://twitter.com/xiaotaoshen1990
@@ -177,10 +93,10 @@ footer:
     left: [package, developed_by, from]
     right: [contact, email, wechat, tidymass]
   components:
-    from: <br> from <i class="fa fa-university"></i> Stanford University <br> <i class="fa fa-clinic-medical"></i>School of Medicine <br> <i class="fa fa-dna"></i> Genetics Department
+    from: <br> from <i class="fa fa-university"></i> Nanyang Technological University Singapore <br> <i class="fa fa-clinic-medical"></i>Lee Kong Chian School of Medicine <br> <i class="fa fa-dna"></i> Genetics Department
     contact: <b>Contact Us:</b> <br>
-    email: <i class="fa fa-envelope"></i> shenxt1990@outlook.com <br>
-    wechat: <i class="fa fa-weixin"></i>  [shenxt1990](https://www.shenxt.info/files/wechat_QR.jpg) <br>
+    email: <i class="fa fa-envelope"></i> xiaotao.shen@outlook.com <br>
+    wechat: <i class="fa fa-weixin"></i>  [jaspershen1990](https://jaspershen.github.io/image/wechat_QR.jpg) <br>
     tidymass: <i class="fa fa-network-wired"></i> [A part of tidymass](https://www.tidymass.org/)