## <script type="text/javascript">
## document.addEventListener("DOMContentLoaded", function() {
##   document.querySelector("h1").style.marginTop = "0";
## });
## </script>
## <script type="text/javascript">
## document.addEventListener("DOMContentLoaded", function() {
##   var links = document.links;  
##   for (var i = 0, linksLength = links.length; i < linksLength; i++)
##     if (links[i].hostname != window.location.hostname)
##       links[i].target = '_blank';
## });
## </script>

Pbase example data

Laurent Gatto

The original data is a 10 fmol Peptide Retention Time Calibration Mixture spiked into 50 ng HeLa background acquired on a Thermo Orbitrap Q Exactive instrument. A restricted set of high scoring human proteins from the UniProt release 2014_06 were searched using the MSGF+ engine.

The fasta database

library("Biostrings")
## Loading required package: XVector
fafile <- system.file("extdata/HUMAN_2014_06-09prots.fasta", package = "Pbase")
fa <- readAAStringSet(fafile)
fa
##   A AAStringSet instance of length 9
##     width seq                                          names               
## [1]   375 MDDDIAALVVDNGSGMCKAGF...WISKQEYDESGPSIVHRKCF sp|P60709|ACTB_HU...
## [2]   664 METPSQRRATRSGAQASSTPL...SYLLGNSSPRTQSPQNCSIM sp|P02545|LMNA_HU...
## [3]   417 MSLSNKLTLDKLDVKGKRVVM...ASLELLEGKVLPGVDALSNI sp|P00558|PGK1_HU...
## [4]  2602 MPVTEKDLAEDAPWKKIQQNT...LAVKWGEEHIPGSPFHVTVP sp|O75369|FLNB_HU...
## [5]   911 MVDYHAANQSYQYGPSSAGNG...VPGALDYKSFSTALYGESDL sp|O43707|ACTN4_H...
## [6]  2624 MFRRARLSVKPNVRPGVGARG...ATTVSEYFFNDIFIEVDETE sp|A6H8Y1|BDP1_HU...
## [7]  3374 MSPESGHSRIFEATAGPNKPE...TLSKDSLSNGVPSGRQAEFS sp|A4UGR9|XIRP2_H...
## [8]   364 MPYQYPALTPEQKKELSDIAH...PSGQAGAAASESLFVSNHAY sp|P04075|ALDOA_H...
## [9]   418 MARRKPEGSSFNMTHLSMAMA...PSGQAGAAASESLFVSNHAY sp|P04075-2|ALDOA...

The PSM data

library("mzID")
idfile <- system.file("extdata/Thermo_Hela_PRTC_1_selected.mzid", package = "Pbase")
id <- flatten(mzID(idfile))
## reading Thermo_Hela_PRTC_1_selected.mzid... DONE!
dim(id)
## [1] 137  41
head(id)
##     spectrumid scan number(s)
## 1    index=173          12256
## 1.1  index=173          12256
## 2    index=163          11860
## 2.1  index=163          11860
## 3    index=200          13408
## 3.1  index=200          13408
##                                                                                spectrum title
## 1   msLevel 2; retentionTime 2094.56706; scanNum 12256; precMz 1137.06665029649; precCharge 2
## 1.1 msLevel 2; retentionTime 2094.56706; scanNum 12256; precMz 1137.06665029649; precCharge 2
## 2   msLevel 2; retentionTime 2039.84424; scanNum 11860; precMz 1136.57450195803; precCharge 2
## 2.1 msLevel 2; retentionTime 2039.84424; scanNum 11860; precMz 1136.57450195803; precCharge 2
## 3   msLevel 2; retentionTime 2258.27868; scanNum 13408; precMz 703.038108542133; precCharge 3
## 3.1 msLevel 2; retentionTime 2258.27868; scanNum 13408; precMz 703.038108542133; precCharge 3
##     acquisitionnum passthreshold rank calculatedmasstocharge
## 1              173          TRUE    1               1136.574
## 1.1            173          TRUE    1               1136.574
## 2              163          TRUE    1               1136.574
## 2.1            163          TRUE    1               1136.574
## 3              200          TRUE    1                703.037
## 3.1            200          TRUE    1                703.037
##     experimentalmasstocharge chargestate ms-gf:denovoscore ms-gf:evalue
## 1                  1137.0667           2               132 2.597097e-18
## 1.1                1137.0667           2               132 2.597097e-18
## 2                  1136.5745           2               230 4.942664e-17
## 2.1                1136.5745           2               230 4.942664e-17
## 3                   703.0381           3               145 4.080429e-10
## 3.1                 703.0381           3               145 4.080429e-10
##     ms-gf:rawscore ms-gf:specevalue assumeddissociationmethod
## 1              118     2.276758e-22                       CID
## 1.1            118     2.276758e-22                       CID
## 2              186     4.333009e-21                       CID
## 2.1            186     4.333009e-21                       CID
## 3               98     3.578068e-14                       CID
## 3.1             98     3.578068e-14                       CID
##     ctermioncurrentratio explainedioncurrentratio isotopeerror
## 1              0.5061673                0.5888804            1
## 1.1            0.5061673                0.5888804            1
## 2             0.48202217               0.57532895            0
## 2.1           0.48202217               0.57532895            0
## 3             0.32245573                0.5909792            0
## 3.1           0.32245573                0.5909792            0
##     ms2ioncurrent meanerrorall meanerrortop7 meanrelerrorall
## 1        526864.0    17.757027     4.3787823     -15.7646885
## 1.1      526864.0    17.757027     4.3787823     -15.7646885
## 2       3342169.2    18.029726     5.0083427       -16.59046
## 2.1     3342169.2    18.029726     5.0083427       -16.59046
## 3       5008038.0    22.256987      8.589616       -17.53643
## 3.1     5008038.0    22.256987      8.589616       -17.53643
##     meanrelerrortop7 ntermioncurrentratio nummatchedmainions stdeverrorall
## 1          -3.255431           0.08271315                 25     23.135044
## 1.1        -3.255431           0.08271315                 25     23.135044
## 2          -3.333969           0.09330681                 30     28.647552
## 2.1        -3.333969           0.09330681                 30     28.647552
## 3         -1.7168152            0.2685235                 22      38.71648
## 3.1       -1.7168152            0.2685235                 22      38.71648
##     stdeverrortop7 stdevrelerrorall stdevrelerrortop7 isdecoy post pre end
## 1         3.582861         24.53603          4.627396   FALSE    C   K 134
## 1.1       3.582861         24.53603          4.627396   FALSE    C   K 188
## 2        2.9929223        29.504406          4.788082   FALSE    C   K 134
## 2.1      2.9929223        29.504406          4.788082   FALSE    C   K 188
## 3        2.4928854        41.070827          8.777729   FALSE    Y   K 173
## 3.1      2.4928854        41.070827          8.777729   FALSE    Y   K 227
##     start               accession length
## 1     112   sp|P04075|ALDOA_HUMAN    364
## 1.1   166 sp|P04075-2|ALDOA_HUMAN    418
## 2     112   sp|P04075|ALDOA_HUMAN    364
## 2.1   166 sp|P04075-2|ALDOA_HUMAN    418
## 3     154   sp|P04075|ALDOA_HUMAN    364
## 3.1   208 sp|P04075-2|ALDOA_HUMAN    418
##                                                                description
## 1      Fructose-bisphosphate aldolase A OS=Homo sapiens GN=ALDOA PE=1 SV=2
## 1.1 Isoform 2 of Fructose-bisphosphate aldolase A OS=Homo sapiens GN=ALDOA
## 2      Fructose-bisphosphate aldolase A OS=Homo sapiens GN=ALDOA PE=1 SV=2
## 2.1 Isoform 2 of Fructose-bisphosphate aldolase A OS=Homo sapiens GN=ALDOA
## 3      Fructose-bisphosphate aldolase A OS=Homo sapiens GN=ALDOA PE=1 SV=2
## 3.1 Isoform 2 of Fructose-bisphosphate aldolase A OS=Homo sapiens GN=ALDOA
##                      pepseq modified modification
## 1   GVVPLAGTNGETTTQGLDGLSER    FALSE         <NA>
## 1.1 GVVPLAGTNGETTTQGLDGLSER    FALSE         <NA>
## 2   GVVPLAGTNGETTTQGLDGLSER    FALSE         <NA>
## 2.1 GVVPLAGTNGETTTQGLDGLSER    FALSE         <NA>
## 3      IGEHTPSALAIMENANVLAR    FALSE         <NA>
## 3.1    IGEHTPSALAIMENANVLAR    FALSE         <NA>
##                      spectrumFile                databaseFile
## 1   Thermo_Hela_PRTC_selected.mgf HUMAN_2014_06-09prots.fasta
## 1.1 Thermo_Hela_PRTC_selected.mgf HUMAN_2014_06-09prots.fasta
## 2   Thermo_Hela_PRTC_selected.mgf HUMAN_2014_06-09prots.fasta
## 2.1 Thermo_Hela_PRTC_selected.mgf HUMAN_2014_06-09prots.fasta
## 3   Thermo_Hela_PRTC_selected.mgf HUMAN_2014_06-09prots.fasta
## 3.1 Thermo_Hela_PRTC_selected.mgf HUMAN_2014_06-09prots.fasta

The Proteins object

library("Pbase")
p <- Proteins(fafile)
p <- addIdentificationData(p, idfile)
## Reading 1 identification files:
##   1. /tmp/RtmpLCCWNo/Rinst2bbe339a122a/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
## done.
p
## S4 class type     : Proteins
## Class version     : 0.1
## Created           : Mon Oct 13 21:05:47 2014
## Number of Proteins: 9
## Sequences:
##   [1] A4UGR9 [2] A6H8Y1 ... [8] P04075-2 [9] P60709
## Sequence features:
##   [1] DB [2] AccessionNumber ... [11] Filename [12] npeps
## Peptide features:
##   [1] DB [2] AccessionNumber ... [25] DatabaseSeq [26] filenames

A Proteins object is composed of a set of protein sequences accessible with the aa accessor as well as an optional set of peptides features that are mapped as coordinates along the proteins, available with pranges. The actual peptide sequences can be extraced with pfeatures.

aa(p)
##   A AAStringSet instance of length 9
##     width seq                                          names               
## [1]  3374 MSPESGHSRIFEATAGPNKPE...TLSKDSLSNGVPSGRQAEFS A4UGR9
## [2]  2624 MFRRARLSVKPNVRPGVGARG...ATTVSEYFFNDIFIEVDETE A6H8Y1
## [3]   911 MVDYHAANQSYQYGPSSAGNG...VPGALDYKSFSTALYGESDL O43707
## [4]  2602 MPVTEKDLAEDAPWKKIQQNT...LAVKWGEEHIPGSPFHVTVP O75369
## [5]   417 MSLSNKLTLDKLDVKGKRVVM...ASLELLEGKVLPGVDALSNI P00558
## [6]   664 METPSQRRATRSGAQASSTPL...SYLLGNSSPRTQSPQNCSIM P02545
## [7]   364 MPYQYPALTPEQKKELSDIAH...PSGQAGAAASESLFVSNHAY P04075
## [8]   418 MARRKPEGSSFNMTHLSMAMA...PSGQAGAAASESLFVSNHAY P04075-2
## [9]   375 MDDDIAALVVDNGSGMCKAGF...WISKQEYDESGPSIVHRKCF P60709
pranges(p)
## IRangesList of length 9
## $A4UGR9
## IRanges of length 36
##      start  end width  names
## [1]   2743 2760    18 A4UGR9
## [2]    307  318    12 A4UGR9
## [3]   1858 1870    13 A4UGR9
## [4]   1699 1708    10 A4UGR9
## [5]   2622 2637    16 A4UGR9
## ...    ...  ...   ...    ...
## [32]    20   31    12 A4UGR9
## [33]  1712 1729    18 A4UGR9
## [34]    48   61    14 A4UGR9
## [35]  2082 2094    13 A4UGR9
## [36]  2743 2756    14 A4UGR9
## 
## ...
## <8 more elements>
pfeatures(p)
## AAStringSetList of length 9
## [["A4UGR9"]] QEITQNKSFFSSVKESQR LPVPKDVYSKQR ... QEITQNKSFFSSVK
## [["A6H8Y1"]] EDAEQVALEVDLNQKKRR ETGKENFR ... ARLSVKPNVRPGVGARGSTASNPQRGR
## [["O43707"]] QQRKTFTAWCNSHLR CQKICDQWDALGSLTHSR ... VGWEQLLTTIAR
## [["O75369"]] DLDIIDNYDYSHTVK PFDLVIPFAVRK ... VQAQGPGLKEAFTNK
## [["P00558"]] ELNYFAKALESPER DLMSKAEK QIVWNGPVGVFEWEAFAR FHVEEEGKGKDASGNK GTKALMDEVVK
## [["P02545"]] METPSQRRATR DTSRRLLAEKEREMAEMR ... RATRSGAQASSTPLSPTR
## [["P04075"]] GVVPLAGTNGETTTQGLDGLSER ... YTPSGQAGAAASESLFVSNHAY
## [["P04075-2"]] GVVPLAGTNGETTTQGLDGLSER ... YTPSGQAGAAASESLFVSNHAY
## [["P60709"]] DLTDYLMKILTER

A Proteins instance is further described by general metadata. Protein sequence and peptide features annotations can be accessed with ametadata and pmetadata (or acols and pcols) respectively.

metadata(p)
## $created
## [1] "Mon Oct 13 21:05:47 2014"
head(acols(p))
## DataFrame with 6 rows and 12 columns
##      DB AccessionNumber   EntryName IsoformName
##   <Rle>     <character> <character>       <Rle>
## 1    sp          A4UGR9 XIRP2_HUMAN          NA
## 2    sp          A6H8Y1  BDP1_HUMAN          NA
## 3    sp          O43707 ACTN4_HUMAN          NA
## 4    sp          O75369  FLNB_HUMAN          NA
## 5    sp          P00558  PGK1_HUMAN          NA
## 6    sp          P02545  LMNA_HUMAN          NA
##                                         ProteinName OrganismName GeneName
##                                         <character>        <Rle>    <Rle>
## 1     Xin actin-binding repeat-containing protein 2 Homo sapiens    XIRP2
## 2 Transcription factor TFIIIB component B'' homolog Homo sapiens     BDP1
## 3                                   Alpha-actinin-4 Homo sapiens    ACTN4
## 4                                         Filamin-B Homo sapiens     FLNB
## 5                         Phosphoglycerate kinase 1 Homo sapiens     PGK1
## 6                                      Prelamin-A/C Homo sapiens     LMNA
##            ProteinExistence SequenceVersion Comment
##                       <Rle>           <Rle>   <Rle>
## 1 Evidence at protein level               2      NA
## 2 Evidence at protein level               3      NA
## 3 Evidence at protein level               2      NA
## 4 Evidence at protein level               2      NA
## 5 Evidence at protein level               3      NA
## 6 Evidence at protein level               1      NA
##                                                                      Filename
##                                                                         <Rle>
## 1 /tmp/RtmpLCCWNo/Rinst2bbe339a122a/Pbase/extdata/HUMAN_2014_06-09prots.fasta
## 2 /tmp/RtmpLCCWNo/Rinst2bbe339a122a/Pbase/extdata/HUMAN_2014_06-09prots.fasta
## 3 /tmp/RtmpLCCWNo/Rinst2bbe339a122a/Pbase/extdata/HUMAN_2014_06-09prots.fasta
## 4 /tmp/RtmpLCCWNo/Rinst2bbe339a122a/Pbase/extdata/HUMAN_2014_06-09prots.fasta
## 5 /tmp/RtmpLCCWNo/Rinst2bbe339a122a/Pbase/extdata/HUMAN_2014_06-09prots.fasta
## 6 /tmp/RtmpLCCWNo/Rinst2bbe339a122a/Pbase/extdata/HUMAN_2014_06-09prots.fasta
##       npeps
##   <integer>
## 1        36
## 2        23
## 3         6
## 4        13
## 5         5
## 6        12
head(pcols(p))
## SplitDataFrameList of length 6
## $A4UGR9
## DataFrame with 36 rows and 26 columns
##        DB AccessionNumber   EntryName IsoformName
##     <Rle>     <character> <character>       <Rle>
## 1      sp          A4UGR9 XIRP2_HUMAN          NA
## 2      sp          A4UGR9 XIRP2_HUMAN          NA
## 3      sp          A4UGR9 XIRP2_HUMAN          NA
## 4      sp          A4UGR9 XIRP2_HUMAN          NA
## 5      sp          A4UGR9 XIRP2_HUMAN          NA
## ...   ...             ...         ...         ...
## 32     sp          A4UGR9 XIRP2_HUMAN          NA
## 33     sp          A4UGR9 XIRP2_HUMAN          NA
## 34     sp          A4UGR9 XIRP2_HUMAN          NA
## 35     sp          A4UGR9 XIRP2_HUMAN          NA
## 36     sp          A4UGR9 XIRP2_HUMAN          NA
##                                                             ProteinName
##                                                             <character>
## 1   sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
## 2   sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
## 3   sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
## 4   sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
## 5   sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
## ...                                                                 ...
## 32  sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
## 33  sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
## 34  sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
## 35  sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
## 36  sp|A4UGR9|XIRP2_HUMAN Xin actin-binding repeat-containing protein 2
##     OrganismName GeneName          ProteinExistence SequenceVersion
##            <Rle>    <Rle>                     <Rle>           <Rle>
## 1   Homo sapiens    XIRP2 Evidence at protein level               2
## 2   Homo sapiens    XIRP2 Evidence at protein level               2
## 3   Homo sapiens    XIRP2 Evidence at protein level               2
## 4   Homo sapiens    XIRP2 Evidence at protein level               2
## 5   Homo sapiens    XIRP2 Evidence at protein level               2
## ...          ...      ...                       ...             ...
## 32  Homo sapiens    XIRP2 Evidence at protein level               2
## 33  Homo sapiens    XIRP2 Evidence at protein level               2
## 34  Homo sapiens    XIRP2 Evidence at protein level               2
## 35  Homo sapiens    XIRP2 Evidence at protein level               2
## 36  Homo sapiens    XIRP2 Evidence at protein level               2
##     Comment spectrumID chargeState      rank passThreshold
##       <Rle>   <factor>   <integer> <integer>     <logical>
## 1        NA  index=124           3         1          TRUE
## 2        NA   index=28           2         1          TRUE
## 3        NA   index=20           2         1          TRUE
## 4        NA  index=187           2         1          TRUE
## 5        NA  index=211           3         1          TRUE
## ...     ...        ...         ...       ...           ...
## 32       NA   index=99           2         1          TRUE
## 33       NA    index=9           2         1          TRUE
## 34       NA  index=122           2         1          TRUE
## 35       NA   index=87           2         1          TRUE
## 36       NA   index=77           2         1          TRUE
##     experimentalMassToCharge calculatedMassToCharge           sequence
##                    <numeric>              <numeric>           <factor>
## 1                   715.0305               715.0308 QEITQNKSFFSSVKESQR
## 2                   715.9177               715.4117       LPVPKDVYSKQR
## 3                   786.9066               786.9081      EQNNDALEKSLRR
## 4                   629.8380               629.3386         SLKESSHRWK
## 5                   645.3429               645.3511   LKMVPRKQREFSGSDR
## ...                      ...                    ...                ...
## 32                  619.2888               618.7782       PESGFAEDSAAR
## 33                 1014.0198              1013.5117 QPDAIPGDIEKAIECLEK
## 34                  821.4005               820.8909     MARYQAAVSRGDCR
## 35                  720.3445               720.3527      TNTSTGLKMAMER
## 36                  821.9231               821.9254     QEITQNKSFFSSVK
##        modNum   isDecoy     post      pre     start       end
##     <integer> <logical> <factor> <factor> <integer> <integer>
## 1           0     FALSE        D        K      2743      2760
## 2           0     FALSE        N        R       307       318
## 3           0     FALSE        L        R      1858      1870
## 4           0     FALSE        E        K      1699      1708
## 5           0     FALSE        G        K      2622      2637
## ...       ...       ...      ...      ...       ...       ...
## 32          0     FALSE        G        K        20        31
## 33          1     FALSE        A        K      1712      1729
## 34          1     FALSE        S        R        48        61
## 35          0     FALSE        S        K      2082      2094
## 36          0     FALSE        E        K      2743      2756
##            DatabaseAccess DatabaseSeq
##                  <factor>    <factor>
## 1   sp|A4UGR9|XIRP2_HUMAN            
## 2   sp|A4UGR9|XIRP2_HUMAN            
## 3   sp|A4UGR9|XIRP2_HUMAN            
## 4   sp|A4UGR9|XIRP2_HUMAN            
## 5   sp|A4UGR9|XIRP2_HUMAN            
## ...                   ...         ...
## 32  sp|A4UGR9|XIRP2_HUMAN            
## 33  sp|A4UGR9|XIRP2_HUMAN            
## 34  sp|A4UGR9|XIRP2_HUMAN            
## 35  sp|A4UGR9|XIRP2_HUMAN            
## 36  sp|A4UGR9|XIRP2_HUMAN            
##                                                                            filenames
##                                                                                <Rle>
## 1   /tmp/RtmpLCCWNo/Rinst2bbe339a122a/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
## 2   /tmp/RtmpLCCWNo/Rinst2bbe339a122a/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
## 3   /tmp/RtmpLCCWNo/Rinst2bbe339a122a/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
## 4   /tmp/RtmpLCCWNo/Rinst2bbe339a122a/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
## 5   /tmp/RtmpLCCWNo/Rinst2bbe339a122a/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
## ...                                                                              ...
## 32  /tmp/RtmpLCCWNo/Rinst2bbe339a122a/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
## 33  /tmp/RtmpLCCWNo/Rinst2bbe339a122a/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
## 34  /tmp/RtmpLCCWNo/Rinst2bbe339a122a/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
## 35  /tmp/RtmpLCCWNo/Rinst2bbe339a122a/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
## 36  /tmp/RtmpLCCWNo/Rinst2bbe339a122a/Pbase/extdata/Thermo_Hela_PRTC_1_selected.mzid
## 
## ...
## <5 more elements>

Specific proteins can be extracted by index of name using [ and proteins and their peptide features can be plotted with the default plot method.

seqnames(p)
## [1] "A4UGR9"   "A6H8Y1"   "O43707"   "O75369"   "P00558"   "P02545"  
## [7] "P04075"   "P04075-2" "P60709"
plot(p[c(1,9)])

plot of chunk pplot

More details can be found in ?Proteins. The object generated above is also directly available as data(p).

Session information

sessionInfo()
## R version 3.1.1 Patched (2014-09-25 r66681)
## Platform: x86_64-unknown-linux-gnu (64-bit)
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
##  [1] stats4    grid      parallel  stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] mzID_1.4.0           Biostrings_2.34.0    XVector_0.6.0       
##  [4] Pbase_0.4.0          Gviz_1.10.0          GenomicRanges_1.18.0
##  [7] GenomeInfoDb_1.2.0   IRanges_2.0.0        S4Vectors_0.4.0     
## [10] Rcpp_0.11.3          BiocGenerics_0.12.0  BiocStyle_1.4.0     
## 
## loaded via a namespace (and not attached):
##  [1] AnnotationDbi_1.28.0     BBmisc_1.7              
##  [3] BSgenome_1.34.0          BatchJobs_1.4           
##  [5] Biobase_2.26.0           BiocInstaller_1.16.0    
##  [7] BiocParallel_1.0.0       DBI_0.3.1               
##  [9] Formula_1.1-2            GenomicAlignments_1.2.0 
## [11] GenomicFeatures_1.18.0   Hmisc_3.14-5            
## [13] MALDIquant_1.11          MASS_7.3-35             
## [15] MSnbase_1.14.0           Pviz_1.0.0              
## [17] R.methodsS3_1.6.1        RColorBrewer_1.0-5      
## [19] RCurl_1.95-4.3           RSQLite_0.11.4          
## [21] Rsamtools_1.18.0         VariantAnnotation_1.12.0
## [23] XML_3.98-1.1             acepack_1.3-3.3         
## [25] affy_1.44.0              affyio_1.34.0           
## [27] base64enc_0.1-2          biomaRt_2.22.0          
## [29] biovizBase_1.14.0        bitops_1.0-6            
## [31] brew_1.0-6               checkmate_1.4           
## [33] chron_2.3-45             cleaver_1.4.0           
## [35] cluster_1.15.3           codetools_0.2-9         
## [37] colorspace_1.2-4         data.table_1.9.4        
## [39] dichromat_2.0-0          digest_0.6.4            
## [41] doParallel_1.0.8         evaluate_0.5.5          
## [43] fail_1.2                 foreach_1.4.2           
## [45] foreign_0.8-61           formatR_1.0             
## [47] ggplot2_1.0.0            gtable_0.1.2            
## [49] impute_1.40.0            iterators_1.0.7         
## [51] knitr_1.7                lattice_0.20-29         
## [53] latticeExtra_0.6-26      limma_3.22.0            
## [55] matrixStats_0.10.0       munsell_0.4.2           
## [57] mzR_2.0.0                nnet_7.3-8              
## [59] pcaMethods_1.56.0        plyr_1.8.1              
## [61] preprocessCore_1.28.0    proto_0.3-10            
## [63] reshape2_1.4             rpart_4.1-8             
## [65] rtracklayer_1.26.0       scales_0.2.4            
## [67] sendmailR_1.2-1          splines_3.1.1           
## [69] stringr_0.6.2            survival_2.37-7         
## [71] tools_3.1.1              vsn_3.34.0              
## [73] zlibbioc_1.12.0