Add example input file for DIANN PTM converter

R/converters.R

@@ -20,7 +20,8 @@
 #' @param protein_id_col Use 'Protein.Groups'(default) column for protein name. 
 #' @param fasta_protein_name Name of column that matches with the protein names 
 #' in `protein_id_col`. The protein names in these two columns must match in 
-#' order to join the FASTA file with the DIA-NN output.
+#' order to join the FASTA file with the DIA-NN output. Default is "uniprot_ac"
+#' for uniprot ID. For uniprot mnemonic ID, use "entry_name"
 #' @param global_qvalue_cutoff The global qvalue cutoff. Default is 0.01.
 #' @param qvalue_cutoff local qvalue cutoff for library. Default is 0.01.
 #' @param pg_qvalue_cutoff local qvalue cutoff for protein groups Run should be 
@@ -46,14 +47,26 @@
 #' @export
 #' 
 #' @examples
-#' # ptm = read.csv("Phospho/report.tsv", sep="\t")
-#' # protein = read.csv("Protein/report.tsv", sep="\t")
-#' # annotation = read.csv("Phospho/annotation.csv")
-#' # annotation_protein = read.csv("Protein/annotation.csv")
+#' # Example from PRIDE ID PXD053502
+#' input = system.file("tinytest/raw_data/DIANN/report.tsv", 
+#'                                         package = "MSstatsPTM")
+#' input = data.table::fread(input)
+#' annot = system.file("tinytest/raw_data/DIANN/annot.csv", 
+#'                                         package = "MSstatsPTM")
+#' annot = data.table::fread(annot)
+#' fasta_path = system.file("extdata", "diann.fasta", 
+#'                        package="MSstatsPTM")
+#' 
+#' msstatsptm_format = DIANNtoMSstatsPTMFormat(
+#'     input, 
+#'     annot, 
+#'     protein_id_col = "Protein.Names", 
+#'     fasta_path = fasta_path, 
+#'     fasta_protein_name = "entry_name", 
+#'     use_log_file = FALSE
+#' )
 #' 
-#' #DIANNtoMSstatsPTMFormat(ptm, annotation, 
-#' #                        protein, annotation_protein,
-#' #                        fasta_path="fasta_file.fasta")
+#' head(msstatsptm_format$PTM)
 #' 
 DIANNtoMSstatsPTMFormat = function(input,
                                    annotation,

inst/extdata/diann.fasta

@@ -0,0 +1,53 @@
+>sp|P25440|BRD2_HUMAN Bromodomain-containing protein 2 OS=Homo sapiens OX=9606 GN=BRD2 PE=1 SV=2
+MLQNVTPHNKLPGEGNAGLLGLGPEAAAPGKRIRKPSLLYEGFESPTMASVPALQLTPAN
+PPPPEVSNPKKPGRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQP
+MDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASM
+PQEEQELVVTIPKNSHKKGAKLAALQGSVTSAHQVPAVSSVSHTALYTPPPEIPTTVLNI
+PHPSVISSPLLKSLHSAGPPLLAVTAAPPAQPLAKKKGVKRKADTTTPTPTAILAPGSPA
+SPPGSLEPKAARLPPMRRESGRPIKPPRKDLPDSQQQHQSSKKGKLSEQLKHCNGILKEL
+LSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRL
+MFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPDEPLEPGPLPVSTAMPPGLAKSSSES
+SSEESSSESSSEEEEEEDEEDEEEEESESSDSEEERAHRLAELQEQLRAVHEQLAALSQG
+PISKPKRKREKKEKKKKRKAEKHRGRAGADEDDKGPRAPRPPQPKKSKKASGSGGGSAAL
+GPSGFGPSGGSGTKLPKKATKTAPPALPTGYDSEEEEESRPMSYDEKRQLSLDINKLPGE
+KLGRVVHIIQAREPSLRDSNPEEIEIDFETLKPSTLRELERYVLSCLRKKPRKPYTIKKP
+VGKTKEELALEKKRELEKRLQDVSGQLNSTKKPPKKANEKTESSSAQQVAVSRLSASSSS
+SDSSSSSSSSSSSDTSDSDSG
+>sp|Q15059|BRD3_HUMAN Bromodomain-containing protein 3 OS=Homo sapiens OX=9606 GN=BRD3 PE=1 SV=1
+MSTATTVAPAGIPATPGPVNPPPPEVSNPSKPGRKTNQLQYMQNVVVKTLWKHQFAWPFY
+QPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTD
+DIVLMAQALEKIFLQKVAQMPQEEVELLPPAPKGKGRKPAAGAQSAGTQQVAAVSSVSPA
+TPFQSVPPTVSQTPVIAATPVPTITANVTSVPVPPAAAPPPPATPIVPVVPPTPPVVKKK
+GVKRKADTTTPTTSAITASRSESPPPLSDPKQAKVVARRESGGRPIKPPKKDLEDGEVPQ
+HAGKKGKLSEHLRYCDSILREMLSKKHAAYAWPFYKPVDAEALELHDYHDIIKHPMDLST
+VKRKMDGREYPDAQGFAADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDEPV
+EAPALPAPAAPMVSKGAESSRSSEESSSDSGSSDSEEERATRLAELQEQLKAVHEQLAAL
+SQAPVNKPKKKKEKKEKEKKKKDKEKEKEKHKVKAEEEKKAKVAPPAKQAQQKKAPAKKA
+NSTTTAGRQLKKGGKQASASYDSEEEEEGLPMSYDEKRQLSLDINRLPGEKLGRVVHIIQ
+SREPSLRDSNPDEIEIDFETLKPTTLRELERYVKSCLQKKQRKPFSASGKKQAAKSKEEL
+AQEKKKELEKRLQDVSGQLSSSKKPARKEKPGSAPSGGPSRLSSSSSSESGSSSSSGSSS
+DSSDSE
+>sp|O60885|BRD4_HUMAN Bromodomain-containing protein 4 OS=Homo sapiens OX=9606 GN=BRD4 PE=1 SV=2
+MSAESGPGTRLRNLPVMGDGLETSQMSTTQAQAQPQPANAASTNPPPPETSNPNKPKRQT
+NQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYW
+NAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEETEIMIVQAKGRG
+RGRKETGTAKPGVSTVPNTTQASTPPQTQTPQPNPPPVQATPHPFPAVTPDLIVQTPVMT
+VVPPQPLQTPPPVPPQPQPPPAPAPQPVQSHPPIIAATPQPVKTKKGVKRKADTTTPTTI
+DPIHEPPSLPPEPKTTKLGQRRESSRPVKPPKKDVPDSQQHPAPEKSSKVSEQLKCCSGI
+LKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGA
+DVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDEPEEPVVAVSSPAVPPPTKVV
+APPSSSDSSSDSSSDSDSSTDDSEEERAQRLAELQEQLKAVHEQLAALSQPQQNKPKKKE
+KDKKEKKKEKHKRKEEVEENKKSKAKEPPPKKTKKNNSSNSNVSKKEPAPMKSKPPPTYE
+SEEEDKCKPMSYEEKRQLSLDINKLPGEKLGRVVHIIQSREPSLKNSNPDEIEIDFETLK
+PSTLRELERYVTSCLRKKRKPQAEKVDVIAGSSKMKGFSSSESESSSESSSSDSEDSETE
+MAPKSKKKGHPGREQKKHHHHHHQQMQQAPAPVPQQPPPPPQQPPPPPPPQQQQQPPPPP
+PPPSMPQQAAPAMKSSPPPFIATQVPVLEPQLPGSVFDPIGHFTQPILHLPQPELPPHLP
+QPPEHSTPPHLNQHAVVSPPALHNALPQQPSRPSNRAAALPPKPARPPAVSPALTQTPLL
+PQPPMAQPPQVLLEDEEPPAPPLTSMQMQLYLQQLQKVQPPTPLLPSVKVQSQPPPPLPP
+PPHPSVQQQLQQQPPPPPPPQPQPPPQQQHQPPPRPVHLQPMQFSTHIQQPPPPQGQQPP
+HPPPGQQPPPPQPAKPQQVIQHHHSPRHHKSDPYSTGHLREAPSPLMIHSPQMSQFQSLT
+HQSPPQQNVQPKKQELRAASVVQPQPLVVVKEEKIHSPIIRSEPFSPSLRPEPPKHPESI
+KAPVHLPQRPEMKPVDVGRPVIRPPEQNAPPPGAPDKDKQKQEPKTPVAPKKDLKIKNMG
+SWASLVQKHPTTPSSTAKSSSDSFEQFRRAAREKEEREKALKAQAEHAEKEKERLRQERM
+RSREDEDALEQARRAHEEARRRQEQQQQQRQEQQQQQQQQAAAVAAAATPQAQSSQPQSM
+LDQQRELARKREQERRRREAMAATIDMNFQSDLLSIFEENLF

inst/tinytest/raw_data/DIANN/annot.csv

@@ -0,0 +1,7 @@
+"Run","Condition","BioReplicate"
+"144-2024-GS-DMSO-R1","DMSO",1
+"144-2024-GS-DMSO-R2","DMSO",2
+"144-2024-GS-DMSO-R3","DMSO",3
+"144-2024-GS-MZ1-R1","MZ-1",4
+"144-2024-GS-MZ1-R2","MZ-1",5
+"144-2024-GS-MZ1-R3","MZ-1",6