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Last data update: 2014.03.03

R: Flatten an mzID related class into a table

flatten

R Documentation

Flatten an mzID related class into a table

Description

This function flattens the content of the object into a table by merging the content intelligently (it knows the links between the different objects).

Usage

flatten(object, safeNames = TRUE)

## S4 method for signature 'mzIDpsm'
flatten(object, safeNames = TRUE)

## S4 method for signature 'mzIDpeptides'
flatten(object, safeNames = TRUE)

## S4 method for signature 'mzID'
flatten(object, safeNames = TRUE)

## S4 method for signature 'mzIDCollection'
flatten(object, safeNames = TRUE)

Arguments

`object`	The object to be flattened
`safeNames`	Logical. Should column names be lowered to ensure compitability between different versions of the mzIdentML schema. Defaults to TRUE

Value

A data.frame with the flattened result or a list of data.frames

Methods (by class)

mzIDpsm: Merge id and scans according to the mapping
mzIDpeptides: Merge peptides with their modifications
mzID: Flatten an mzID object with respect to psm'
mzIDCollection: Flatten all mzID object in the collection into a list of data frames.

Examples

exampleFile <- system.file('extdata', '55merge_tandem.mzid', package = 'mzID')
mzResults <- mzID(exampleFile)
head(flatten(mzResults))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(mzID)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mzID/flatten.Rd_%03d_medium.png", width=480, height=480)
> ### Name: flatten
> ### Title: Flatten an mzID related class into a table
> ### Aliases: flatten flatten,mzID-method flatten,mzIDCollection-method
> ###   flatten,mzIDpeptides-method flatten,mzIDpsm-method
> 
> ### ** Examples
> 
> exampleFile <- system.file('extdata', '55merge_tandem.mzid', package = 'mzID')
> mzResults <- mzID(exampleFile)
reading 55merge_tandem.mzid... DONE!
> head(flatten(mzResults))
  spectrumid     spectrum title acquisitionnum passthreshold rank
1   index=12 55.1074.1074.3.dta             12         FALSE    1
2  index=285   55.884.884.3.dta            285         FALSE    1
3   index=83 55.3471.3474.3.dta             83         FALSE    1
4   index=21 55.1145.1145.3.dta             21         FALSE    1
5  index=198   55.721.761.3.dta            198         FALSE    1
6   index=13 55.1103.1106.2.dta             13         FALSE    1
  calculatedmasstocharge experimentalmasstocharge chargestate x\!tandem:expect
1               903.4032                 903.7209           3           0.00017
2               792.3899                 792.3792           3           0.00290
3               792.3899                 792.5295           3           0.00300
4               849.7635                 850.0782           3           0.00510
5               527.2849                 527.2592           3           0.01600
6               724.3771                 724.8816           2           0.06700
  x\!tandem:hyperscore isdecoy post pre end start             accession length
1                  79.6   FALSE    S   K 239   217     psu|NC_LIV_020800    376
2                  70.3   FALSE    L   R 313   292     psu|NC_LIV_020800    376
3                  70.1   FALSE    L   R 313   292     psu|NC_LIV_020800    376
4                  44.8   FALSE    V   K 865   842     psu|NC_LIV_105380   1028
5                  51.2   FALSE    R   R 311   297     psu|NC_LIV_140010    316
6                  27.5    TRUE    D   K 404   392 Rnd3psu|NC_LIV_113200   2167
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 sequence
1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                MADEEVQALVVDNGSGNVKAGVAGDDAPRAVFPSIVGKPKNPGIMVGMEEKDCYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANRERMTQIMFETFNVPAMYVAIQAVLSLYSSGRTTGIVLDSGDGVSHTVPIYEGYALPHAIMRLDLAGRDLTEYMMKILHERGYGFTTSAEKEIVRDIKEKLCYIALDFDEEMKAAEDSSDIEKSYELPDGNIITVGNERFRCPEALFQPSFLGKEAAGVHRTTFDSIMKCDVDIRKDLYGNVVLSGGTTMYEGIGERLTKELTSLAPSTMKIKVVAPPERKYSVWIGGSILSSLSTFQQMWITKEEYDESGPSIVHRKCF
2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                MADEEVQALVVDNGSGNVKAGVAGDDAPRAVFPSIVGKPKNPGIMVGMEEKDCYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANRERMTQIMFETFNVPAMYVAIQAVLSLYSSGRTTGIVLDSGDGVSHTVPIYEGYALPHAIMRLDLAGRDLTEYMMKILHERGYGFTTSAEKEIVRDIKEKLCYIALDFDEEMKAAEDSSDIEKSYELPDGNIITVGNERFRCPEALFQPSFLGKEAAGVHRTTFDSIMKCDVDIRKDLYGNVVLSGGTTMYEGIGERLTKELTSLAPSTMKIKVVAPPERKYSVWIGGSILSSLSTFQQMWITKEEYDESGPSIVHRKCF
3                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                MADEEVQALVVDNGSGNVKAGVAGDDAPRAVFPSIVGKPKNPGIMVGMEEKDCYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANRERMTQIMFETFNVPAMYVAIQAVLSLYSSGRTTGIVLDSGDGVSHTVPIYEGYALPHAIMRLDLAGRDLTEYMMKILHERGYGFTTSAEKEIVRDIKEKLCYIALDFDEEMKAAEDSSDIEKSYELPDGNIITVGNERFRCPEALFQPSFLGKEAAGVHRTTFDSIMKCDVDIRKDLYGNVVLSGGTTMYEGIGERLTKELTSLAPSTMKIKVVAPPERKYSVWIGGSILSSLSTFQQMWITKEEYDESGPSIVHRKCF
4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    MTRGKKHPKQGLSFRVPESCCFSFCESVSGRQLNSLVKPPTLSTPFPTGAFFPPSPVSCVFAAFSQAERTMSSFTGPSSVRLRPGVLCVFLSLLSLSLTCVPFSPSSLSLPSSLPSSLPAAYGIRLDAAQPVPPQPDSLPVAGATDSCREPAGAFDGADGVPSLREAEEILRREQTVATEHAQRAAEDVQQFAEAAREAAAKGDIAAAHELAAAAAAAAAEAQDIAAYAQAVSETDPALLRERAQEEAHRSAESEARRQQAASESQANAAEQGLPYGSCDVTITPDDIASVPEALEKLAALETSVQEAGEQLDEKEQMVAEYMLAASEAAERHDEASRAFEDAKKQKKENLAAAAEKEALEAAAEYEELATAVQVLTEEAEAQSGKALADAVAAGEMRYAINQKIVSDADPAARGKVPRSLLAPKHFHISDAASGRVLKIYFHNSFAPFDDLPCAALHTDAYLCRQHPRCVVQYEQSGDEVLQRCILDDAYLWLVASTSDFCAAAPEGSSQAAASPFDNATPLEPMAAVTEEEIEAVALDLLQESGVDGPAVLEQMAKDGKSTSDLCGFVQALSAELLRTERDPRCASPADDGENIALTTEALLASNFGFLGPAAPATASPSASAAAPAPRSASIRSHNRNAFAAGGAGKNAFAPVPRISPSGLFGLLGGSSAKANAPIRMGINGMGRIGRLVFRIAMTRPDVTVTHINCSMDPAYIAYMLKYDSVHGRFDGEIVPTDSGLIVNGQEVSISNTRDPEEIPWAAQGADYVCESTGVFCTTEAAAKHVNRPGGAKHAVISAPAKDESTPTLVVGVNAEQDYESSMKVVSCASCTTNGLAPLVKVIDENFGLVEGLMTTVHAATGTQKVVDGTSKKDWRGGRAATGNIIPSSTGAAKAVARCLPHMKGKLTGMAFRVPTLDVSVVDLTCRLNKSTTYEEIKKAVREASETYMRGIIGYTEEPIVSQDIVGSQCSTVFDANAGIMLNPNFVKLVSWYDNEYAYSARLVDLIAVMAAKDGVVAAGTGLDRKPF
5                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            MAAPSAAPSSSADFRAQSKSFLQDFLMGGVAGGISKTVVAPIERVKLLLQLQDASTQIGHQAGQIRKYEGLKDCFVRVYREQGFLSFWRGNWANVVRYFPTQALNFACKEKYQKLFVRHDPKKDFWKFFAEMLAAGGAAGATSLAFVYPLDFARTRLGADVGKVQAERQFTGLNDCIQKIYKEFGIPGLYRGFLVSVAGIIVYRAAFFGLYDTAKAVLPSDKKTSHPVMRNFAIGLGVETAAGVIAYPFDTVRRRMMMQALRSDTLYRNTWNCASRIVREEGITAYYKGCGSNVVRGVGGAIVLVLYDEMKRFVAP
6 ALFNWFHFTQSVAYRADKAGEAEAAAFARASDALLMTASAHRQRRPAGRNPSIPGQTPASFAQPDTDADVLPQAEKERPFVVGRGTYNRQDTPEVTRGFAGLADQRSRANSLSERQGESEDQKGANFQLYGDVLALWRMPFAVQDYMFLNEGARSTVPDQPRDMIAKNQLGENDAVPLNSLRALVNAVYEKLTAEEQGAINGQRLRFTRISALRQLSVQRLAVIAAMAQNSKNGRDSAEAAAPTRQAGRGRGNLNRSIYLGRDATLADWCRRRALDTDDEYRATASKGLGTIAPSEGRSIDLWIGPAWVRVHGLGGVRREAARLIEVTRAKPVALTSWMGPRLGPEPLRLGALFCQGIAELDDLDRSETVPTARQLERGARQLTQSLAVDKHAVGGRYSSLLCKDFPQNDRNLTMAAMRCASELAEERQETRRNPARGGLSLRSSLGESFARLQLNTTANPKLSGCAPGDREMGAEPGRCAAPRAAANLGRRELLSTVGLVSEGRLRVEEEAFTSVFRSHPTGRRDLTVAENSQVRVNERSGQAEADFARRVLMGLRTAENEVSEAAPAGACRAASQESPRRDSKPSESGSSFGGSLRRERVMTSEGVAPQQARPSGAVGARPPGVPPLASTAGGNSSGREASVEERPKHTHGSETKFAQMIESRHLYYPLGRAGYRLSGARQVLSATSSSCLRRELAFPGGPTGEVLRGRASRGPDILPKAEVAIATSSHFGDSSDKGGAERQDRGSHDTFPLTYRLQLGGRMRACAEIHRDQALASPPSPRELREAIGGGGRQTGVEGRDSMRAKRLREQQSTRLQDGARVIFPGRPGLRVVVNPIPWDGINVGPQASRSKGFPVGEFKSQSAKLTENRIDLNLQVTKSKIGLPSSVSELETYSLAWRASSDLLFRCAESQKNRQIKETRDVHVIALGIWNSALLGERGEGLDHEESLTAQSLTRSPGAGASLPALSESGFLLSASRAPRLVLGVGVELTGETRTGRVANGYHRTLELIGSKPVVYVALPGILGSSADAQHAKPLHFGKSLLLEANLGNRVATRAKAGCQAGQRRGLETREHDLLRRRFGGSTGDSSNSLQFGILRHRVYAIASNKLARSYRDIVENSRQEMGGRGANQGKVRYQSSLKKVKSRKGQTVKRFILCASGQRGRALKKSLGAKKKVLTRLDNCYKMKQSTRVVNTDARARQALECSRLLGFRLKSQSGARSEESALGRRRAKKKLVSEARRWMKASVKHTDERRATAAGNRRTGDLANKLCLNALKQGERASDGRAKDVGVVRRGRISSAGAVGVLERQALLRREHFGRKRVAYRLKKKGWVYEYATATIKKTHERSKNRAADSLESAKKRISALKKAGEENRKLMSENAMELRGKSGTGRRSCLAGNMKKKKVEVMLRSNLESGSSVASERAAKDGKWVTCGAKRRGSVDKKGALLTWCEKSRSARVHSGELTARQADGGARFKGSGLRQRHVYLAVRIRLRLCSHSWRTSARDQSARQRFKTKASNFGLQKLRVEGSRSLALHRLRLDAAKAGSTRRQLSADRLALAIDFRKTRAYHRLFAAFDMAQTRIVAEVLDRSLNSLKSSMIGLSQAIRSRAGSSFVRDAAGAISVAQVYRATGILAAAMKVELCQAGVRSGDRTTSGLLRGRRERDAVASFIQDKVKDSKAKIFAERGRRVGTENENGSKVSLVISKKGRLGAHKKSNQLRTHAIRDAGDTEKFARSRDAHFSGEAARGCVYCLKQTYKRAKGTAQQCDINDRRKLSARSGASDRRMRFSQHRVREHGLQSKAAKARWVQGTADAKDEKTTADFGACRREDTLQVANDMRSPLQGRPLARSLSRLFVLFGSRVLVAWKVRESKKETSFERARAALDVRRARNYDASTFLGPKPEGERRLQLPGSFGQRLSLKFGRHLELRQEAAAKSEEAKRTAAVMFRALKRPLESEISGFVNEQSAGGLFALDRLRAGSTLLISGKPDKASKETALKRLQAERWEPLARQSSKYFLPPVNAVRILGSFRTSGVEQSKIETRRPQRAHGANIRKPPADDFEGEASRGGVSPNKEQPEPVAAPAAVMPARKEVGVGICESGTMRSDVEQETRAQKAVCLKKLSVDRRECVDEQFRSFPPLTSPGEKTSLADLARPELQGVMSAVLYREV
                    pepseq modified              modification
1  LCYIALDFDEEMKAAEDSSDIEK     TRUE 57.0215 (2), 15.9949 (12)
2   KDLYGNVVLSGGTTMYEGIGER     TRUE              15.9949 (15)
3   KDLYGNVVLSGGTTMYEGIGER     TRUE              15.9949 (15)
4 VIDENFGLVEGLMTTVHAATGTQK     TRUE              15.9949 (13)
5          GVGGAIVLVLYDEMK     TRUE              15.9949 (14)
6            HAVGGRYSSLLCK     TRUE              57.0215 (12)
               idFile spectrumFile                 databaseFile
1 55merge_tandem.mzid  55merge.mgf Neo_rndTryp_3times.fasta.pro
2 55merge_tandem.mzid  55merge.mgf Neo_rndTryp_3times.fasta.pro
3 55merge_tandem.mzid  55merge.mgf Neo_rndTryp_3times.fasta.pro
4 55merge_tandem.mzid  55merge.mgf Neo_rndTryp_3times.fasta.pro
5 55merge_tandem.mzid  55merge.mgf Neo_rndTryp_3times.fasta.pro
6 55merge_tandem.mzid  55merge.mgf Neo_rndTryp_3times.fasta.pro
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>