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Properties of sample analyses

Source: R/main.R, R/utils-exported.R
analysis-information.Rd

Properties for the sample analyses used in the workflow and utilities to automatically generate this information.

Usage

generateAnalysisInfo(
  fromRaw = NULL,
  fromCentroid = NULL,
  fromProfile = NULL,
  fromIMS = NULL,
  convCentroid = NULL,
  convProfile = NULL,
  convIMS = NULL,
  ...
)

generateAnalysisInfoFromEnviMass(path)

Arguments

fromRaw, fromCentroid, fromProfile, fromIMS

One or more file paths that should be used for finding analyses that are stored as raw, centroided, profile or IMS data, respectively (see details below). Set to NULL to skip file detection for a particular file type.

convCentroid, convProfile, convIMS

These arguments specify the MS file conversion destination paths for centroided, profile and IMS data, respectively. These paths are used for those analyses for which no file with a particular file type could be found in the directories specified by the respective from* arguments. Set to NULL to not set any destination directory. If multiple paths are specified then these will be recycled to fill the table rows.

...

Any other columns that should be added to the analysis information table, such as replicate and blank. The arguments specified by ... should be named. Vectors are recycled to the number of rows of the table.

path

The path of the enviMass project.

Value

generateAnalysisInformation returns a data.frame with automatically generated analysis information.

Details

In patRoon a sample analysis, or simply analysis, refers to a single MS analysis file (sometimes also called sample or file). The analysis information summarizes several properties for the analyses, and is used in various steps throughout the workflow, such as findFeatures, averaging intensities of feature groups and blank subtraction. The analysis information should be a data.frame or data.table with a set of mandatory and optional columns (described below).

generateAnalysisInfo is an utility function that automatically generates analysis information. It scans given directories for analysis files, and uses this to automatically fill in the analysis and path_* columns. This function automatically groups together analyses that are stored with different file types and formats (see further details below).

generateAnalysisInfoFromEnviMass loads analysis information from an enviMass project. Note: this funtionality has only been tested with older versions of enviMass.

Mandatory analysis information columns

The following columns should be present in the analysis information:

  • path_raw, path_centroid, path_profile, path_ims Specifies the directory path for the raw, centroided, profile and IMS data, respectively. See below for more details. At least one column should not be empty for each row.

  • analysis the file name without extension and without directory path. Must be unique across all table rows.

  • replicate name of the replicate. Used to group analyses together that are replicates of each other. Thus, the replicate column for all analyses considered to be belonging to the same replicate should have an equal (but unique) value. Used for e.g. averaging and filter.

  • blank all analyses within this replicate are used by the featureGroups method of filter for blank subtraction. Multiple entries can be entered by separation with a comma. May be empty ("") if no blank subtraction is desired.

Analysis paths, file types and file formats

Depending on the workflow step, different file types for the same analysis may be required.

  • raw Specifies the directory to raw HRMS files (e.g. .raw, .d). This is used by e.g. conversion of raw MS data and the OpenTIMS backend.

  • centroid Specifies the directory to centroided and exported HRMS files (.mzML, .mzXML). These files are required by most feature finding algorithms.

  • profile Specifies the directory to exported but not centroided (i.e. profile) HRMS data files (.mzML, .mzXML). This is currently only used by findFeaturesSAFD.

  • ims Specifies the directory to exported IMS-HRMS data (.mzML). This is required in IMS workflows, unless raw IMS-HRMS data is directly loaded with the OpenTIMS backend. See e.g. assignMobilities for more details.

Some workflows may require multiple file formats for a same file type. In this case, the file formats should be stored within the same directory specified by the respective path_* column. For instance, if feature finding algorithms from OpenMS and enviPick are mixed then centroided .mzML and .mzXML files are needed, and files with both file formats must be stored in the directory specified by path_centroid.

If non-raw data files are not yet present and should be exported by MS file conversion, then path_centroid, path_profile and path_ims should specify the desired destination paths of the converted files.

Optional columns and sample metadata

The following columns may need to be present:

  • conc a numeric value specifying the 'concentration' for the analysis. This can be actually any kind of numeric value such as exposure time, dilution factor or anything else which may be used to form a linear relationship. This is used by the as.data.table method if regression=TRUE. As of patRoon version 3.0, any other column than "conc" can be used by setting its name with the regression argument.

  • norm_conc a numeric value specifying the normalization concentration for the analysis. See the Feature intensity normalization section in the featureGroups documentation) for more details.

Any other columns that are present will be added to the features and featureGroups objects as metadata. This metadata can be used e.g. in various plotting and data subsetting functions.