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

Description Usage Arguments Value Examples

View source: R/CUSUMChart.R

Description

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

Usage

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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

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# 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")
CUSUMChart(data = sampleData, peptide = "LVNELTEFAK", metric = "Peak Assymetry")

eralpdogu/MSstatsQC documentation built on Nov. 21, 2018, 10:21 p.m.