getNodeRun {DIAlignR} | R Documentation

## Create a child run from two parent runs

### Description

Get merged features and merged chromatograms from parent runs. Chromatograms are written on the disk at dataPath/xics. For each precursor aligned parent time-vectors and corresponding child time-vector are also calculated and written as *_av.rda at dataPath.

### Usage

    getNodeRun(
      runA,
      runB,
      mergeName,
      dataPath,
      fileInfo,
      features,
      mzPntrs,
      prec2chromIndex,
      precursors,
      params,
      adaptiveRTs,
      refRuns,
      multipeptide,
      peptideScores,
      ropenms,
      applyFun = lapply
    )

### Arguments

`runA` | (string) name of a run to be merged with runB. Must be in the rownames of fileInfo.
`runB` | (string) name of a run to be merged with runA. Must be in the rownames of fileInfo.
`mergeName` | (string) name of the node that is generated with merging of runA and runB.
`dataPath` | (string) path to xics and osw directory.
`fileInfo` | (data-frame) output of `getRunNames`.
`features` | (list of data-frames) contains features and their properties identified in each run.
`mzPntrs` | (list) a list of mzRpwiz.
`prec2chromIndex` | (list) a list of dataframes having following columns: transition_group_id: it is PRECURSOR.ID from osw file. chromatogramIndex: index of chromatogram in mzML file.
`precursors` | (data-frame) atleast two columns transition_group_id and transition_ids are required.
`params` | (list) parameters are entered as list. Output of the `paramsDIAlignR` function.
`adaptiveRTs` | (environment) an empty environment used to store data for downstream analysis.
`refRuns` | (environment) an empty environment used to store data for downstream analysis.
`multipeptide` | (environment) contains multiple data-frames that are collection of features associated with analytes. This is an output of `getMultipeptide`.
`peptideScores` | (list of data-frames) each dataframe has scores of a peptide across all runs.
`ropenms` | (pyopenms module) get this python module through `get_ropenms`. Required only for chrom.mzML files.
`applyFun` | (function) value must be either lapply or BiocParallel::bplapply.

### Value

(None)

### Author(s)

Shubham Gupta, shubh.gupta@mail.utoronto.ca

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-06-06

### See Also

`childXICs, getChildXICs, traverseUp`

### Examples

    library(data.table)
    dataPath <- system.file("extdata", package = "DIAlignR")
    params <- paramsDIAlignR()
    fileInfo <- getRunNames(dataPath = dataPath)
    mzPntrs <- list2env(getMZMLpointers(fileInfo))
    precursors <- getPrecursors(fileInfo, oswMerged = TRUE, runType = params[["runType"]],
     context = "experiment-wide", maxPeptideFdr = params[["maxPeptideFdr"]])
    peptideIDs <- unique(precursors$peptide_id)
    peptideScores <- getPeptideScores(fileInfo, peptideIDs, oswMerged = TRUE, params[["runType"]], params[["context"]])
    masters <- paste("master", 1:(nrow(fileInfo)-1), sep = "")
    peptideScores <- lapply(peptideIDs, function(pep) {x <- peptideScores[.(pep)][,-c(1L)]
      x <- rbindlist(list(x, data.table("run" = masters, "score" = NA_real_, "pvalue" = NA_real_,
        "qvalue" = NA_real_)), use.names=TRUE)
      setkeyv(x, "run"); x})
    names(peptideScores) <- as.character(peptideIDs)
    features <- getFeatures(fileInfo, maxFdrQuery = 1.00, runType = "DIA_Proteomics")
    ## Not run:
    masterFeatures <- dummyFeatures(precursors, nrow(fileInfo)-1, 1L)
    features <- do.call(c, list(features, masterFeatures))
    multipeptide <- getMultipeptide(precursors, features, numMerge = 0L, startIdx = 1L)
    prec2chromIndex <- getChromatogramIndices(fileInfo, precursors, mzPntrs)
    masterChromIndex <- dummyChromIndex(precursors, nrow(fileInfo)-1, 1L)
    prec2chromIndex <- do.call(c, list(prec2chromIndex, masterChromIndex))
    mergeName <- "master1"
    adaptiveRTs <- new.env()
    refRuns <- new.env()
    getNodeRun(runA = "run2", runB = "run0", mergeName = mergeName, dataPath = ".", fileInfo, features,
     mzPntrs, prec2chromIndex, precursors, params, adaptiveRTs, refRuns, multipeptide, peptideScores, ropenms = NULL)
    file.remove(file.path(".", "xics", paste0(mergeName, ".chrom.sqMass")))
    file.remove(list.files(".", pattern = "*_av.rds", full.names = TRUE))

    ## End(Not run)
    for(run in names(mzPntrs)) DBI::dbDisconnect(mzPntrs[[run]])

[Package DIAlignR version 2.2.0 Index]