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AnalysisInfo data.frame methods

Source: R/analysisInfo.R
analysisinfo-dataframe.Rd

Various parsing and plotting functions for the analysisInfo data.frame.

Usage

# S4 method for class 'data.frame'
getTICs(obj, retentionRange = NULL, MSLevel = 1)

# S4 method for class 'data.frame'
getBPCs(obj, retentionRange = NULL, MSLevel = 1)

# S4 method for class 'data.frame'
plotTICs(
  obj,
  retentionRange = NULL,
  MSLevel = 1,
  retMin = FALSE,
  title = NULL,
  groupBy = NULL,
  showLegend = TRUE,
  xlim = NULL,
  ylim = NULL,
  ...
)

# S4 method for class 'data.frame'
plotBPCs(
  obj,
  retentionRange = NULL,
  MSLevel = 1,
  retMin = FALSE,
  title = NULL,
  groupBy = NULL,
  showLegend = TRUE,
  xlim = NULL,
  ylim = NULL,
  ...
)

# S4 method for class 'data.table'
plotTICs(
  obj,
  retentionRange = NULL,
  MSLevel = 1,
  retMin = FALSE,
  title = NULL,
  groupBy = NULL,
  showLegend = TRUE,
  xlim = NULL,
  ylim = NULL,
  ...
)

# S4 method for class 'data.table'
plotBPCs(
  obj,
  retentionRange = NULL,
  MSLevel = 1,
  retMin = FALSE,
  title = NULL,
  groupBy = NULL,
  showLegend = TRUE,
  xlim = NULL,
  ylim = NULL,
  ...
)

Arguments

obj

An analysisInfo data.frame object as obtained by generateAnalysisInfo function.

retentionRange

Range of retention time (in seconds), m/z, respectively. Should be a numeric vector with length of two containing the min/max values. The maximum can be Inf to specify no maximum range. Set to NULL to skip this step.

MSLevel

Integer vector with the ms levels (i.e., 1 for MS1 and 2 for MS2) to obtain traces.

retMin

Plot retention time in minutes (instead of seconds).

title

Character string used for title of the plot. If NULL a title will be automatically generated.

groupBy

Specifies how results are grouped in the plot. Should be a name of a column in the analysis information table which is used to make analysis groups (e.g. "replicate"), or "fGroups" to group by feature group. Set to NULL for no grouping.

showLegend

Plot a legend if TRUE.

xlim, ylim

Sets the plot size limits used by plot. Set to NULL for automatic plot sizing.

...

Further arguments passed to plot.

Functions

  • getTICs(data.frame): Obtain the total ion chromatogram/s (TICs) of the analyses.

  • getBPCs(data.frame): Obtain the base peak chromatogram/s (BPCs) of the analyses.

  • plotTICs(data.frame): Plots the TICs of the analyses.

  • plotBPCs(data.frame): Plots the BPCs of the analyses.

  • plotBPCs(data.table): Plots the BPCs of the analyses.

Use of raw HRMS data

The raw data interface of patRoon is used by these functions to process HRMS (or IMS-HRMS) data. Please see its documentation for more information on the supported formats and available configuration options.

Author

Ricardo Cunha (cunha@iuta.de) and Rick Helmus (r.helmus@uva.nl)