profMat-xcmsSet: The profile matrix

In sneumann/xcms: LC-MS and GC-MS Data Analysis

The profile matrix

Description

The profile matrix is an n x m matrix, n (rows) representing equally spaced m/z values (bins) and m (columns) the retention time of the corresponding scans. Each cell contains the maximum intensity measured for the specific scan and m/z values falling within the m/z bin.

The `profMat` method creates a new profile matrix or returns the
profile matrix within the object's `@env` slot, if available.
Settings for the profile matrix generation, such as `step` (the bin
size), `method` or additional settings are extracted from the
respective slots of the `xcmsRaw` object.
Alternatively it is possible to specify all of the settings as
additional parameters.

For [MsExperiment()] or [XcmsExperiment()] objects, the method returns
a `list` of profile matrices, one for each sample in `object`. Using
parameter `fileIndex` it is also possible to create a profile matrix only
for selected samples (files).

Usage

## S4 method for signature 'MsExperiment'
profMat(
  object,
  method = "bin",
  step = 0.1,
  baselevel = NULL,
  basespace = NULL,
  mzrange. = NULL,
  fileIndex = seq_along(object),
  chunkSize = 1L,
  msLevel = 1L,
  BPPARAM = bpparam(),
  ...
)

## S4 method for signature 'xcmsRaw'
profMat(object, method, step, baselevel, basespace, mzrange.)

Arguments

object	An xcmsRaw, OnDiskMSnExp, XCMSnExp, MsExperiment or XcmsExperiment object.
method	character(1) defining the profile matrix generation method. Allowed are "bin", "binlin", "binlinbase" and "intlin". See details section for more information.
step	numeric(1) representing the m/z bin size.
baselevel	numeric(1) representing the base value to which empty elements (i.e. m/z bins without a measured intensity) should be set. Only considered if method = "binlinbase". See baseValue parameter of imputeLinInterpol() for more details.
basespace	numeric(1) representing the m/z length after which the signal will drop to the base level. Linear interpolation will be used between consecutive data points falling within 2 * basespace to each other. Only considered if method = "binlinbase". If not specified, it defaults to 0.075. Internally this parameter is translated into the distance parameter of the imputeLinInterpol() function by distance = floor(basespace / step). See distance parameter of imputeLinInterpol() for more details.
mzrange.	Optional numeric(2) manually specifying the mz value range to be used for binnind. If not provided, the whole m/z value range is used.
fileIndex	For MsExperiment or XcmsExperiment: integer defining the idex (or indices) of the sample(s) from which the profile matrix should be created.
chunkSize	For MsExperiment or XcmsExperiment: integer(1) defining the number of files from which data should be loaded and processed in one iteration. By default one file at a time is processed chunkSize = 1L which requires less memory. For parallel processing, the chunkSize should be >= than the number of parallel processes that should be used.
msLevel	For MsExperiment or XcmsExperiment: integer(1) defining the MS level from which the profile matrix should be generated.
BPPARAM	For MsExperiment or XcmsExperiment: parallel processing setup. See bpparam() for more details. Defaults to BPPARAM = bpparam().
...	ignored.

Details

Profile matrix generation methods:

• "bin": The default profile matrix generation method that does a simple binning, i.e. aggregating of intensity values falling within an m/z bin.

• "binlin": Binning followed by linear interpolation to impute missing values. The value for m/z bins without a measured intensity are inferred by a linear interpolation between neighboring bins with a measured intensity.

• "binlinbase": Binning followed by a linear interpolation to impute values for empty elements (m/z bins) within a user-definable proximity to non-empty elements while stetting the element's value to the baselevel otherwise. See impute = "linbase" parameter of imputeLinInterpol() for more details.

• "intlin": Set the elements' values to the integral of the linearly interpolated data from plus to minus half the step size.

Value

profMat returns the profile matrix (rows representing scans, columns equally spaced m/z values). For object being a MsExperiment or XcmsExperiment, the method returns a list of profile matrices, one for each file (sample).

Author(s)

Johannes Rainer

Examples

file <- system.file('cdf/KO/ko15.CDF', package = "faahKO")
## Load the data without generating the profile matrix (profstep = 0)
xraw <- xcmsRaw(file, profstep = 0)
## Extract the profile matrix
profmat <- profMat(xraw, step = 0.3)
dim(profmat)
## If not otherwise specified, the settings from the xraw object are used:
profinfo(xraw)
## To extract a profile matrix with linear interpolation use
profmat <- profMat(xraw, step = 0.3, method = "binlin")
## Alternatively, the profMethod of the xraw objects could be changed
profMethod(xraw) <- "binlin"
profmat_2 <- profMat(xraw, step = 0.3)
all.equal(profmat, profmat_2)

sneumann/xcms documentation built on Nov. 23, 2024, 6:53 p.m.