XmRChart {MSstatsQC} | R Documentation |
A function to construct individual (X) and moving range (mR) control charts
XmRChart(data = NULL, peptide, L = 1, U = 5, metric, normalization = FALSE, ytitle = "Individual observations", type = "mean", selectMean = NULL, selectSD = NULL)
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. |
A plot of individual values or moving ranges versus time per peptide and metric generated from XmR.data.prepare
data frame.
# 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")