CUSUMChart {MSstatsQC} | R Documentation

## A function to create cumulative sum charts for mean (CUSUMm) and cumulative sum charts for variability (CUSUMv) control charts

### Description

A function to create cumulative sum charts for mean (CUSUMm) and cumulative sum charts for variability (CUSUMv) control charts

### Usage

    CUSUMChart(
      data = NULL,
      peptide,
      L = 1,
      U = 5,
      metric,
      normalization = TRUE,
      ytitle = "CUSUMm",
      type = "mean",
      selectMean = NULL,
      selectSD = NULL,
      referenceValue = 0.5,
      decisionInterval = 5
    )

### Arguments

`data` | comma-separated (.csv), metric file. It should contain a "Precursor" column and the metrics columns. It should also include "Annotations" for each observation.
`peptide` | the name of precursor of interest.
`L` | Lower bound of the guide set.
`U` | Upper bound of the guide set.
`metric` | the name of metric of interest.
`normalization` | TRUE if metric is standardized and FALSE if not standardized.
`ytitle` | the y-axis title of the plot. Defaults to "CUSUMm". The x-axis title is by default "Time : name of peptide"
`type` | the type of the control chart. Two values can be assigned, "mean" or "variability". Default is "mean"
`selectMean` | the mean of a metric. It is used when mean is known. It is NULL when mean is not known. The default is NULL.
`selectSD` | the standard deviation of a metric. It is used when standard deviation is known. It is NULL when mean is not known. The default is NULL.
`referenceValue` | the value that is used to tune the control chart for a proper shift size
`decisionInterval` | the threshold to detect an out-of-control observation

### Value

A plot of pozitive and negative CUSUM statistics versus time per peptide and metric generated from `CUSUM.data.prepare` data frame.

### Examples

    # First process the data to make sure it's ready to use
    sampleData <- DataProcess(S9Site54)
    head(sampleData)
    # Find the name of the peptides
    levels(sampleData$Precursor)
    # Calculate CUSUM statistics
    CUSUMChart(data = sampleData, peptide = "VLVLDTDYK", metric = "BestRetentionTime")
    CUSUMChart(data = sampleData, peptide = "VLVLDTDYK", metric = "BestRetentionTime",
               ytitle = "CUSUMv", type = "variability")
    CUSUMChart(data = sampleData, peptide = "VLVLDTDYK", metric = "BestRetentionTime",
               selectMean = 27.78, selectSD = 8.19)
    CUSUMChart(data = sampleData, peptide = "DDGSWEVIEGYR", metric = "TotalArea")
    CUSUMChart(data = sampleData, peptide = "DDGSWEVIEGYR", metric = "TotalArea",
               selectMean = 35097129, selectSD = 34132861)
    CUSUMChart(data = sampleData, peptide = "TAAYVNAIEK", metric = "MaxFWHM")

[Package MSstatsQC version 2.8.0 Index]