betweenAlignment: Data Structure for "between" alignment of many GCMS samples

In rromoli/flagme: Analysis of Metabolomics GC/MS Data

Data Structure for "between" alignment of many GCMS samples

Description

This function creates a "between" alignment (i.e. comparing merged peaks)

Usage

betweenAlignment(
  pD,
  cAList,
  pAList,
  impList,
  filterMin = 1,
  gap = 0.7,
  D = 10,
  usePeaks = TRUE,
  df = 30,
  verbose = TRUE,
  metric = 2,
  type = 2,
  penality = 0.2,
  compress = FALSE
)

Arguments

pD	a peaksDataset object
cAList	list of clusterAlignment objects, one for each experimental group
pAList	list of progressiveAlignment objects, one for each experimental group
impList	list of imputation lists
filterMin	minimum number of peaks within a merged peak to be kept in the analysis
gap	gap parameter
D	retention time penalty parameter
usePeaks	logical, whether to use peaks (if TRUE) or the full 2D profile alignment (if FALSE)
df	distance from diagonal to calculate similarity
verbose	logical, whether to print information
metric	numeric, different algorithm to calculate the similarity matrix between two mass spectrum. metric=1 call normDotProduct(); metric=2 call ndpRT(); metric=3 call corPrt()
type	numeric, two different type of alignment function
penality	penalization applied to the matching between two mass spectra if (t1-t2)>D
compress	logical whether to compress the similarity matrix into a sparse format.

Details

betweenAlignment objects gives the data structure which stores the result of an alignment across several "pseudo" datasets. These pseudo datasets are constructed by merging the "within" alignments.

Value

betweenAlignment object

Author(s)

Mark Robinson

References

Mark D Robinson (2008). Methods for the analysis of gas chromatography - mass spectrometry data PhD dissertation University of Melbourne.

See Also

multipleAlignment

Examples

	require(gcspikelite)
	## see 'multipleAlignment'

rromoli/flagme documentation built on Feb. 10, 2023, 12:59 a.m.