metabData: Constructor for the metabData object.

In hhabra/Combiner: Method for Combining LC-MS Metabolomics Feature Measurements

Constructor for the metabData object.

Description

This is a constructor for objects of type metabData.

Usage

metabData(
  table,
  mz = "mz",
  rt = "rt",
  id = "id",
  adduct = "adduct",
  samples = NULL,
  Q = NULL,
  extra = NULL,
  rtmin = "min",
  rtmax = "max",
  misspc = 50,
  measure = c("median", "mean"),
  zero = FALSE,
  duplicate = opts.duplicate()
)

Arguments

table	Path to file containing feature table or data.frame object containing features
mz	Character name(s) or regular expression associated with data column containing m/z values. The first column whose name contains this expression will be selected for analysis.
rt	Character name(s) or regular expression associated with data column containing retention time values. The first column whose name contains this expression will be selected for analysis.
id	Character name(s) or regular expression associated with data column containing metabolomics feature identifiers. The first column whose name contains this expression will be selected for analysis.
adduct	Character name(s) or regular expression associated with data column containing adduct or chemical formula annotations. The first column whose name contains this expression will be selected for analysis.
samples	Character name(s) or regular expression associated with data columns. All numeric columns whose names contain these keywords are selected for analysis. If no keywords given, program searches longest stretch of remaining numeric columns.
Q	Character name(s) or regular expression associated with numeric feature abundance quantiles. If NULL, abundance quantiles are calculated from sample intensities.
extra	Character names of columns containing additional feature information, e.g. non-analyzed sample values. All columns containing these keywords selected and will be displayed in the final output.
rtmin	Numeric. Minimum retention time for analysis.
rtmax	Numeric. Maximum retention time for analysis.
misspc	Numeric. Threshold missingness percentage for analysis.
measure	Central sample abundance measure, either "median" or "mean".
zero	Logical. Whether to consider zero values as missing.
duplicate	list of duplicate feature removal parameters. (see: opts.duplicate)

Details

Processed metabolomics feature table must contain columns for m/z, rt, and numeric sample intensities. Some optional fields such as identity id and adduct label columns may also be supplied. Non-analyzed columns can be included into the final output by specifying the names of these columns in the extra argument. All required arguments are checked for validity (e.g. no negative m/z or rt values, each column is used at most once, column types are valid, etc...).

Following this is a pre-analysis filtering of rows that are either: 1) Outside of a specified retention time range (rtmin,rtmax), 2) Missing in excess of misspc percent of analyzed samples, or 3) deemed duplicates by small pairwise <m/z, rt> differences. See: opts.duplicate on duplicate feature removal

Remaining features are ranked by abundance quantiles, Q, using a central measure, either "median" or "mean." Alternatively, the abundance quantiles column can be specified in the argument Q.

Value

An object of class metabData containing the specific information specified by mz,rt, samples, id, adduct, Q, and extra arguments, and adjusted by pre-processing steps.

Examples

data(plasma30)
data(plasma20)

#samples: CHEAR; RedCross samples non-analyzed "extra" columns
p30 <- metabData(plasma30, mz = "mz", rt = "rt", id = "identity",
                 adduct = "adduct", samples = "CHEAR", extra = "RedCross")

getSamples(p30)  #should print names of 5 CHEAR Sample column names
getExtra(p30)    #should print names of 5 Red Cross Sample column names

#equivalent to above
p30 <- metabData(plasma30, id = "id", samples = "CHEAR", extra = "Red")

#analyzing Red Cross samples with retention time limitations (0.5-17.5min)
p20 <- metabData(plasma20, samples = "Red", rtmin = 0.5, rtmax = 17.5)
data = getData(p20)
range(data$rt)

#using regular expressions for field searches
p30 <- metabData(plasma30, id = "identity|id|ID", samples = ".[3-5]$")
getSamples(p30)    #should print all column names ending in .3, .4, .5

hhabra/Combiner documentation built on June 5, 2024, 10:56 a.m.