MSTperBatch {DIAlignR} | R Documentation

## Aligns an analyte for a batch of peptides

### Description

For the ith analyte in the batch, this function traverse the MST from start node and align runs pairwise. In the process it updates multipeptide with aligned features.

### Usage

    MSTperBatch(
      iBatch,
      nets,
      peptides,
      multipeptide,
      refRuns,
      precursors,
      prec2chromIndex,
      fileInfo,
      mzPntrs,
      params,
      globalFits,
      RSE,
      applyFun = lapply
    )

### Arguments

`nets` | (list) set of trees ordered for traversal obained from `traverseMST`.
`peptides` | (integer) vector of peptide IDs.
`multipeptide` | (list) contains multiple data-frames that are collection of features associated with analytes. This is an output of `getMultipeptide`.
`refRuns` | (data-frame) output of `getRefRun`. Must have two columsn : transition_group_id and run.
`precursors` | (data-frame) atleast two columns transition_group_id and transition_ids are required.
`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.
`fileInfo` | (data-frame) output of `getRunNames`.
`mzPntrs` | (list) a list of mzRpwiz.
`params` | (list) parameters are entered as list. Output of the `paramsDIAlignR` function.
`globalFits` | (list) each element is either of class lm or loess. This is an output of `getGlobalFits`.
`RSE` | (list) Each element represents Residual Standard Error of corresponding fit in globalFits.

### Value

invisible NULL

### Author(s)

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

ORCID: 0000-0003-3500-8152

License: (c) Author (2021) + GPL-3 Date: 2021-05-15

### See Also

`mstAlignRuns, alignToRefMST, getAlignedTimesFast, getMultipeptide`

### Examples

    dataPath <- system.file("extdata", package = "DIAlignR")

[Package DIAlignR version 2.2.0 Index]