Man pages for wolski/imsbInfer
Visualization, normalization and QC of proteomics SWATH-MS data
| aggregatePeptides | aggregate peptides |
| aggregateProteins | aggregate peptides - given msexperiment with transitons |
| analyzeDuplicated | analyse duplicated peptides/proteins |
| analyzeDuplicatedPeptides | analyse duplicated peptides - same peptide different charge |
| analyzeDuplicatedProteins | analyse duplicated protein peptide - same protein id... |
| analyzeDuplicatedProteinsTOP | analyse duplicated protein peptides - same protein id... |
| compPeptideCorrelations | compute various correlation |
| convert2msExperiment | converts to msExperiment (exported more for debugging... |
| convert2MSstats | convert to MSstats |
| convertLF2Wideformat | convert LF 2 wide format |
| correctIntRTv1 | correct intensity over RT for entire msexperiment |
| correctIntRTv1.default | correct intensity over RT for entire msexperiment |
| correctIntRTv1.matrix | correct intensity over RT for entire msexperiment |
| correctIntRTv1.msexperiment | correct intensity over RT for entire msexperiment |
| correctIntRTv2.default | correct Intensity RT using func, i.e. runrobscale (default) |
| correctIntRTv2.msexperiment | correct intensity over RT for entire msexperiment |
| dim.msexperiment | dimension |
| dimnames.msexperiment | show colnames (it does'nt let you set the columns) |
| feature_alignment_requant | feature_alignment_requant - output of feature aligner requant |
| filterByScore | filter rows by qscore |
| getListOfDuplicated | find duplicated entries in vector |
| getListOfDuplicatedOrderedByIntensity | get a list of duplicates (their indices) ordered by intensity |
| getUniqueEntries | get a list of of unique entries in rownames |
| imsbInfer | A package with some utility functions for the analysis of... |
| keepRTRange | removes unwanted RT ranges |
| keepRTRange.msexperiment | filter data given RT range |
| loadTransitonsMSExperiment | load msexperiment with nrt transtions and peptides |
| mycolnames | allows to set colnames for all the matrices in msexperiment |
| orderByKey | order by Key |
| orderByKey.msexperiment | orders rows by rowkey |
| orderByRT | order by RT |
| orderByRT.msexperiment | orders rows by retention time of peptide |
| pairsDifference | plot x-y against retention time |
| pairsRatio | plot log2(x/y) against retention time |
| plotPairCors | plot the output of compPeptideCorrelations |
| prepareDF | checks input file for required columns - removes nonrequired... |
| randomPairs | sample pairs from pepidx |
| read2msExperiment.data.frame | convert data.frame 2 msexperiment |
| read2msExperiment.default | read 2 feature alginer long format and generate an... |
| removeDecoys | remove decoys |
| removeDecoys.msexperiment | remove decoys and decoy column from msexperiment |
| removeSample | remove sample from dataset |
| removeSamples | remove a specific samples from the dataset |
| reordercolumns | reorders all the matrices by the columnnames |
| SDat | SDat - example of an msexperiment class |
| selectTopFragmentsPerPeptide | selecting top transtions WARNING - slow running function |
| selectTopPeptidesPerProtein | this function selects the top x peptides / protein |
| setRequantToNA | removes requant values from dataset |
| setRequantToNA.msexperiment | removes requant values from dataset |
| subset.msexperiment | subset data given idx vector |
| summaryCors | summaryCors |
| transitions2wide | extract transition intensities from input file. WARNING -... |
