diff --git a/articles/LFQ_parse_qc_protein_inference.html b/articles/LFQ_parse_qc_protein_inference.html index fd65f96..6ecacf4 100644 --- a/articles/LFQ_parse_qc_protein_inference.html +++ b/articles/LFQ_parse_qc_protein_inference.html @@ -84,7 +84,7 @@

LFQ QC and summarisation to protein-level abundance

Tom Smith

-

2023-01-17

+

2024-07-01

@@ -359,8 +359,8 @@

QC peptides= 0.7 # Reduce the column name size ) #> Warning in gplots::heatmap.2(as.matrix(missing_data), col = c("black", -#> "lightgray"), : Discrepancy: Colv is FALSE, while dendrogram is `both'. Omitting -#> column dendogram. +#> "lightgray"), : Discrepancy: Colv is FALSE, while dendrogram is `both'. +#> Omitting column dendogram.
Presence/Absence heatmap

Presence/Absence heatmap @@ -639,7 +639,7 @@

Alternative normal programmatically.

 # remotes::install_github("csdaw/uniprotREST")
-res <- uniprotREST::uniprot_map(
+res <- uniprotREST::uniprot_map(
   ids = rownames(prot_robust),
   fields = c("accession", "feature_count", "go_id"),
   format = "tsv",
@@ -747,9 +747,9 @@ 
Alternative normal
 

 
Session info
 

-
#> R version 4.2.2 (2022-10-31)
+
#> R version 4.2.3 (2023-03-15)
 #> Platform: x86_64-pc-linux-gnu (64-bit)
-#> Running under: Ubuntu 22.04.1 LTS
+#> Running under: Ubuntu 22.04.2 LTS
 #> 
 #> Matrix products: default
 #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
@@ -768,50 +768,49 @@ 
Session info#> [8] base     
 #> 
 #> other attached packages:
-#>  [1] httr_1.4.4          tibble_3.1.8        dplyr_1.0.10       
-#>  [4] tidyr_1.2.1         ggplot2_3.4.0       biobroom_1.30.0    
-#>  [7] broom_1.0.2         gplots_3.1.3        naniar_0.6.1       
+#>  [1] httr_1.4.5          tibble_3.2.1        dplyr_1.1.1        
+#>  [4] tidyr_1.3.0         ggplot2_3.4.2       biobroom_1.30.0    
+#>  [7] broom_1.0.4         gplots_3.1.3        naniar_1.0.0       
 #> [10] MSnbase_2.24.2      ProtGenerics_1.30.0 mzR_2.32.0         
-#> [13] Rcpp_1.0.9          Biobase_2.58.0      Biostrings_2.66.0  
-#> [16] GenomeInfoDb_1.34.6 XVector_0.38.0      IRanges_2.32.0     
-#> [19] S4Vectors_0.36.1    BiocGenerics_0.44.0 camprotR_0.0.0.9000
+#> [13] Rcpp_1.0.10         Biobase_2.58.0      Biostrings_2.66.0  
+#> [16] GenomeInfoDb_1.34.9 XVector_0.38.0      IRanges_2.32.0     
+#> [19] S4Vectors_0.36.2    BiocGenerics_0.44.0 camprotR_0.0.0.9000
 #> 
 #> loaded via a namespace (and not attached):
-#>   [1] colorspace_2.0-3       ellipsis_0.3.2         visdat_0.5.3          
-#>   [4] rprojroot_2.0.3        fs_1.5.2               clue_0.3-63           
-#>   [7] farver_2.1.1           affyio_1.68.0          bit64_4.0.5           
-#>  [10] AnnotationDbi_1.60.0   fansi_1.0.3            codetools_0.2-18      
-#>  [13] ncdf4_1.21             doParallel_1.0.17      cachem_1.0.6          
-#>  [16] impute_1.72.2          robustbase_0.95-0      knitr_1.41            
-#>  [19] jsonlite_1.8.4         GO.db_3.16.0           cluster_2.1.4         
-#>  [22] vsn_3.66.0             png_0.1-8              BiocManager_1.30.19   
-#>  [25] compiler_4.2.2         backports_1.4.1        assertthat_0.2.1      
-#>  [28] fastmap_1.1.0          limma_3.54.0           cli_3.6.0             
-#>  [31] htmltools_0.5.4        tools_4.2.2            gtable_0.3.1          
-#>  [34] glue_1.6.2             GenomeInfoDbData_1.2.9 affy_1.76.0           
-#>  [37] rappdirs_0.3.3         MALDIquant_1.22        jquerylib_0.1.4       
-#>  [40] pkgdown_2.0.7          vctrs_0.5.1            preprocessCore_1.60.1 
-#>  [43] iterators_1.0.14       xfun_0.36              stringr_1.5.0         
-#>  [46] lifecycle_1.0.3        iq_1.9.7               gtools_3.9.4          
-#>  [49] XML_3.99-0.13          DEoptimR_1.0-11        zlibbioc_1.44.0       
-#>  [52] MASS_7.3-58.1          scales_1.2.1           ragg_1.2.5            
-#>  [55] pcaMethods_1.90.0      parallel_4.2.2         httr2_0.2.2           
-#>  [58] yaml_2.3.6             curl_5.0.0             memoise_2.0.1         
-#>  [61] gridExtra_2.3          UpSetR_1.4.0           sass_0.4.4            
-#>  [64] RSQLite_2.2.20         stringi_1.7.12         highr_0.10            
-#>  [67] desc_1.4.2             foreach_1.5.2          checkmate_2.1.0       
-#>  [70] caTools_1.18.2         BiocParallel_1.32.5    rlang_1.0.6           
-#>  [73] pkgconfig_2.0.3        systemfonts_1.0.4      bitops_1.0-7          
-#>  [76] mzID_1.36.0            evaluate_0.19          lattice_0.20-45       
-#>  [79] purrr_1.0.1            labeling_0.4.2         bit_4.0.5             
-#>  [82] tidyselect_1.2.0       plyr_1.8.8             magrittr_2.0.3        
-#>  [85] R6_2.5.1               generics_0.1.3         DBI_1.1.3             
-#>  [88] pillar_1.8.1           withr_2.5.0            MsCoreUtils_1.10.0    
-#>  [91] KEGGREST_1.38.0        RCurl_1.98-1.9         crayon_1.5.2          
-#>  [94] KernSmooth_2.23-20     utf8_1.2.2             rmarkdown_2.19        
-#>  [97] grid_4.2.2             blob_1.2.3             uniprotREST_0.0.0.9000
-#> [100] digest_0.6.31          textshaping_0.3.6      munsell_0.5.0         
-#> [103] bslib_0.4.2

+#>   [1] colorspace_2.1-0       visdat_0.6.0           rprojroot_2.0.3       
+#>   [4] fs_1.6.1               clue_0.3-64            farver_2.1.1          
+#>   [7] affyio_1.68.0          bit64_4.0.5            AnnotationDbi_1.60.2  
+#>  [10] fansi_1.0.4            codetools_0.2-19       ncdf4_1.21            
+#>  [13] doParallel_1.0.17      cachem_1.0.7           impute_1.72.3         
+#>  [16] robustbase_0.95-1      knitr_1.42             jsonlite_1.8.4        
+#>  [19] GO.db_3.16.0           cluster_2.1.4          vsn_3.66.0            
+#>  [22] png_0.1-8              BiocManager_1.30.20    compiler_4.2.3        
+#>  [25] backports_1.4.1        fastmap_1.1.1          limma_3.54.2          
+#>  [28] cli_3.6.1              htmltools_0.5.5        tools_4.2.3           
+#>  [31] gtable_0.3.3           glue_1.6.2             GenomeInfoDbData_1.2.9
+#>  [34] affy_1.76.0            rappdirs_0.3.3         MALDIquant_1.22.1     
+#>  [37] jquerylib_0.1.4        pkgdown_2.0.7          vctrs_0.6.2           
+#>  [40] preprocessCore_1.60.2  iterators_1.0.14       xfun_0.38             
+#>  [43] stringr_1.5.0          lifecycle_1.0.3        iq_1.9.10             
+#>  [46] gtools_3.9.4           XML_3.99-0.14          DEoptimR_1.0-12       
+#>  [49] zlibbioc_1.44.0        MASS_7.3-58.3          scales_1.2.1          
+#>  [52] ragg_1.2.5             pcaMethods_1.90.0      parallel_4.2.3        
+#>  [55] httr2_0.2.2            yaml_2.3.7             curl_5.0.0            
+#>  [58] memoise_2.0.1          gridExtra_2.3          UpSetR_1.4.0          
+#>  [61] sass_0.4.5             stringi_1.7.12         RSQLite_2.3.1         
+#>  [64] highr_0.10             desc_1.4.2             foreach_1.5.2         
+#>  [67] checkmate_2.1.0        caTools_1.18.2         BiocParallel_1.32.6   
+#>  [70] rlang_1.1.0            pkgconfig_2.0.3        systemfonts_1.0.4     
+#>  [73] bitops_1.0-7           mzID_1.36.0            evaluate_0.20         
+#>  [76] lattice_0.21-8         purrr_1.0.1            labeling_0.4.2        
+#>  [79] bit_4.0.5              tidyselect_1.2.0       plyr_1.8.8            
+#>  [82] magrittr_2.0.3         R6_2.5.1               generics_0.1.3        
+#>  [85] DBI_1.1.3              pillar_1.9.0           withr_2.5.0           
+#>  [88] MsCoreUtils_1.10.0     KEGGREST_1.38.0        RCurl_1.98-1.12       
+#>  [91] crayon_1.5.2           KernSmooth_2.23-20     utf8_1.2.3            
+#>  [94] rmarkdown_2.21         grid_4.2.3             blob_1.2.4            
+#>  [97] uniprotREST_1.0.0      digest_0.6.31          textshaping_0.3.6     
+#> [100] munsell_0.5.0          bslib_0.4.2

 

 

 
References
diff --git a/articles/SILAC.html b/articles/SILAC.html
index 4054682..a666bf5 100644
--- a/articles/SILAC.html
+++ b/articles/SILAC.html
@@ -83,7 +83,7 @@
       
Processing and QC of SILAC data

                         
Tom Smith

             
-            
2023-01-17

+            
2024-07-01

       
       
       
@@ -446,7 +446,7 @@ 
Processing and QC of SILAC
     psm_matched_data[[psm_name]] %>%
       mutate(replicate = rep_n)
   }) %>% 
-  bind_rows()
+  bind_rows()
 #> [1] "1"
 #> [1] "2"
 #> [1] "3"
diff --git a/articles/TMT_PSM_QC_Summarisation.html b/articles/TMT_PSM_QC_Summarisation.html
index 474c7b2..a40eb15 100644
--- a/articles/TMT_PSM_QC_Summarisation.html
+++ b/articles/TMT_PSM_QC_Summarisation.html
@@ -84,7 +84,7 @@ 
TMT QC PSM-level quantification and
 summarisation to protein-level abundance

                         
Tom Smith

             
-            
2023-01-17

+            
2024-07-01

       
       
       
diff --git a/articles/crap.html b/articles/crap.html
index a325884..1ecc0c1 100644
--- a/articles/crap.html
+++ b/articles/crap.html
@@ -84,7 +84,7 @@ 
cRAP databases

                         
Charlotte
 Dawson

             
-            
2023-01-17

+            
2024-07-01

       
       
       
@@ -223,7 +223,7 @@ 
Cambridge Centre for Prot
 
 ccp_tmp <- tempfile(fileext = ".fasta")
 download_ccp_crap(ccp_tmp, is_crap = TRUE, verbose = TRUE)
-#> Downloading from UniProtKB release: 2022_05

+#> Downloading from UniProtKB release: 2024_03

We can load this FASTA file into R and take a look.

 ccp_crap <- Biostrings::readAAStringSet(ccp_tmp)
@@ -343,7 +343,7 @@ 
Make your own cRAP databasemake_fasta(accessions = c("P00776", "P00777", "P80561"),
                 file = griseus_tmp,
                 is_crap = FALSE)
-#> Downloading from UniProtKB release: 2022_05
+#> Downloading from UniProtKB release: 2024_03

Before we add these to our CCP cRAP FASTA, we just need to take note of what cRAP number the sequences headers stop at.

diff --git a/articles/msnset.html b/articles/msnset.html
index 9f753bd..be3dea5 100644
--- a/articles/msnset.html
+++ b/articles/msnset.html
@@ -84,7 +84,7 @@ 
Working with MSnSets

                         
Charlotte
 Dawson

             
-            
2023-01-17

+            
2024-07-01

       
       
       
@@ -174,7 +174,7 @@ 
Exploring an MSnSet#>   ..@ experimentData   :Formal class 'MIAPE' [package "MSnbase"] with 30 slots
 #>   ..@ processingData   :Formal class 'MSnProcess' [package "MSnbase"] with 10 slots
 #>   ..@ qual             :'data.frame':    220 obs. of  7 variables:
-#>   ..@ assayData        :<environment: 0x55987b14f028> 
+#>   ..@ assayData        :<environment: 0x55d014466db0> 
 #>   ..@ phenoData        :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
 #>   ..@ featureData      :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
 #>   ..@ annotation       : chr "No annotation"
@@ -444,7 +444,7 @@ 
Make the MSnSet#>   ..@ processingData   :Formal class 'MSnProcess' [package "MSnbase"] with 10 slots
 #>   ..@ qual             :'data.frame':    0 obs. of  0 variables
 #> Formal class 'data.frame' [package "methods"] with 4 slots
-#>   ..@ assayData        :<environment: 0x55988e413a10> 
+#>   ..@ assayData        :<environment: 0x55d0271dc2a8> 
 #>   ..@ phenoData        :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
 #>   ..@ featureData      :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
 #>   ..@ annotation       : chr(0) 
diff --git a/authors.html b/authors.html
index 00d0f51..c5e6002 100644
--- a/authors.html
+++ b/authors.html
@@ -78,14 +78,14 @@ 
Citation
-

Dawson C, Smith T (2023). +

Dawson C, Smith T (2024). camprotR: Processing, analysing and visualising CCP proteomics data. R package version 0.0.0.9000. 

@Manual{,
   title = {camprotR: Processing, analysing and visualising CCP proteomics data},
   author = {Charlotte Dawson and Tom Smith},
-  year = {2023},
+  year = {2024},
   note = {R package version 0.0.0.9000},
 }
diff --git a/pkgdown.yml b/pkgdown.yml index bad5ce1..b069489 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -7,5 +7,5 @@ articles: TMT_PSM_QC_Summarisation: TMT_PSM_QC_Summarisation.html crap: crap.html msnset: msnset.html -last_built: 2023-01-17T16:17Z +last_built: 2024-07-01T08:56Z diff --git a/reference/check_uniprot_release.html b/reference/check_uniprot_release.html index 5014c26..60f1f43 100644 --- a/reference/check_uniprot_release.html +++ b/reference/check_uniprot_release.html @@ -84,13 +84,13 @@

Value

Examples

# print release number to console
 check_uniprot_release()
-#> [1] "2022_05"
+#> [1] "2024_03"
 
 # save release number and use in e.g. a file name
 rls <- check_uniprot_release()
 
 paste0("folder/filename_", rls, ".fasta")
-#> [1] "folder/filename_2022_05.fasta"
+#> [1] "folder/filename_2024_03.fasta"
diff --git a/reference/count_features_per_protein.html b/reference/count_features_per_protein.html index ca3d4c1..3d63bd9 100644 --- a/reference/count_features_per_protein.html +++ b/reference/count_features_per_protein.html @@ -121,7 +121,7 @@

Examples

#> 8 126 "A1X283" 1 #> 9 126 "A3KMH1" 1 #> 10 126 "A3KN83" 1 -#> # … with 23,532 more rows +#> # ℹ 23,532 more rows