alignToRef {DIAlignR} | R Documentation

## Aligns an analyte from an experiment to the reference run

### Description

df contains unaligned features for an analyte across multiple runs. This function aligns eXp run to ref run and updates corresponding features.

### Usage

    alignToRef(
      eXp,
      ref,
      refIdx,
      fileInfo,
      XICs,
      XICs.ref,
      params,
      df,
      globalFits,
      RSE
    )

### Arguments

`eXp` | (string) name of the run to be aligned to reference run. Must be in the rownames of fileInfo.
`ref` | (string) name of the reference run. Must be in the rownames of fileInfo.
`refIdx` | (integer) index of the reference feature in df.
`fileInfo` | (data-frame) output of `getRunNames`.
`XICs` | (list of dataframes) fragment-ion chromatograms of the analytes for all runs.
`XICs.ref` | (list of dataframes) fragment-ion chromatograms of the analyte_chr from the reference run.
`params` | (list) parameters are entered as list. Output of the `paramsDIAlignR` function.
`df` | (dataframe) a collection of features related to the peptide
`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 (2020) + GPL-3 Date: 2020-07-26

### See Also

`alignTargetedRuns, perBatch, setAlignmentRank, getMultipeptide`

### Examples

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

[Package DIAlignR version 2.2.0 Index]