n15qc: N15 labelling QC report
In qcmetrics: A Framework for Quality Control

Description Usage Arguments Value Author(s)

View source: R/qc.R

A simple wrapper for the QC of 15N labelling. The respective QC items are the distribution of PSM incorporation rates, distribution of log2 fold-changes and number of identified features. See the vignette for details.

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  n15qc(object,
    fcol = c("Protein_Accession", "Peptide_Sequence", "Number_Of_Unique_Peptides", "Variable_Modifications", "inc"),
    inctr = 97.5, lfctr = c(-0.5, 0.5), type, reportname)

`object`	An `MSnSet` to be quality controlled.
`fcol`	The name of the feature variables for the protein identifiers (accession numbers for example), the peptide sequences, the number of unique peptides for each identified protein, the variable modifications identified on the peptides and the N15 incorporation rate. These must be provided in that order. Defaults are `Protein_Accession`, `Peptide_Sequence`, `Number_Of_Unique_Peptides`, `Variable_Modifications`, and `inc`.
`inctr`	The minimum level of median incorporation rate to set the QC item status to `TRUE`. Default is 97.5.
`lfctr`	The range of accepted median PSM log2 fold-change for the QC item status to be set to `TRUE`. Default is `c(-0.5, 0.5)`.
`type`	The type of report to be saved. If missing (default), no report is generated. See `qcReport` for details.
`reportname`	The name of the report, in case a `type` is defined. If missing (default), the report will be names `n15qcreport` followed by the generation data and time.