XmRChart: A function to construct individual (X) and moving range (mR)...

Description Usage Arguments Value Examples

View source: R/XmRChart.R

Description

A function to construct individual (X) and moving range (mR) control charts

Usage

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XmRChart(data = NULL, peptide, L = 1, U = 5, metric,
  normalization = FALSE, ytitle = "Individual observations",
  type = "mean", selectMean = NULL, selectSD = NULL)

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 "Individual observations". 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.

Value

A plot of individual values or moving ranges versus time per peptide and metric generated from XmR.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 X and mR statistics
XmRChart(data = sampleData, peptide = "VLVLDTDYK", metric = "BestRetentionTime")
XmRChart(data = sampleData, peptide = "VLVLDTDYK", metric = "BestRetentionTime",
         ytitle = "moving ranges", type = "variability")
XmRChart(data = sampleData, peptide = "VLVLDTDYK", metric = "BestRetentionTime",
         selectMean = 27.78, selectSD = 8.19)
XmRChart(data = sampleData, peptide = "DDGSWEVIEGYR", metric = "TotalArea")
XmRChart(data = sampleData, peptide = "DDGSWEVIEGYR", metric = "TotalArea",
         selectMean = 35097129, selectSD = 34132861)
XmRChart(data = sampleData, peptide = "TAAYVNAIEK", metric = "MaxFWHM")
XmRChart(data = sampleData, peptide = "LVNELTEFAK", metric = "Peak Assymetry")

eralpdogu/MSstatsQC documentation built on March 24, 2018, 4:11 a.m.