pickNearestFeature {DIAlignR} | R Documentation

## Pick feature closest to reference peak

### Description

It picks a feature that is within adaptiveRT window across eXpRT and has lowest m-score. Feature's m-score also has to be smaller than featureFDR.

### Usage

    pickNearestFeature(eXpRT, analyte, oswFiles, runname, adaptiveRT,
      featureFDR)

### Arguments

`eXpRT` | (numeric) retention time in experiment run.
`analyte` | (string) analyte is as PRECURSOR.GROUP_LABEL or as PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file.
`oswFiles` | (list of data-frames) it is output from getOswFiles function.
`runname` | (string) must be a combination of "run" and an iteger e.g. "run2".
`adaptiveRT` | (numeric) half-width of retention time window. Feature, if found, is picked from within this window.
`featureFDR` | (numeric) upper m-score cut-off for a feature to be picked.

### Value

(list) Following elements are present in the list:

`leftWidth` | (numeric) as in FEATURE.LEFT_WIDTH of osw files.
`rightWidth` | (numeric) as in FEATURE.RIGHT_WIDTH of osw files.
`RT` | (numeric) retention time as in FEATURE.EXP_RT of osw files.
`Intensity` | (numeric) peak intensity as in FEATURE_MS2.AREA_INTENSITY of osw files.
`peak_group_rank` | (integer) rank of each feature associated with transition_group_id.
`m_score` | (numeric) q-value of each feature associated with transition_group_id.

### Author(s)

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

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-12-13

### See Also

`getOswFiles, getOswAnalytes`

### Examples

    data(oswFiles_DIAlignR, package="DIAlignR")
    ## Not run:
    pickNearestFeature(eXpRT = 5237.8, analyte = "14299_QFNNTDIVLLEDFQK/3",
     oswFiles = oswFiles_DIAlignR, runname = "run2", adaptiveRT = 77.82315, featureFDR = 0.05)

    ## End(Not run)

[Package DIAlignR version 0.99.12 Index]