CUSUMChart: A function to create cumulative sum charts for mean (CUSUMm)...

In eralpdogu/MSstatsQC: Longitudinal system suitability monitoring and quality control for proteomic experiments

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")

eralpdogu/MSstatsQC documentation built on April 17, 2020, 7:33 a.m.