retcor-methods {xcms}R Documentation

Align retention times across samples with Obiwarp

Description

Calculate retention time deviations for each sample. It is based on the code at http://obi-warp.sourceforge.net/. However, this function is able to align multiple samples, by a center-star strategy.

For the original publication see

Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by Ordered Bijective Interpolated Warping John T. Prince and, Edward M. Marcotte Analytical Chemistry 2006 78 (17), 6140-6152

Arguments

object the xcmsSet object
plottype if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density
col vector of colors for plotting each sample
ty vector of line and point types for plotting each sample
profStep step size (in m/z) to use for profile generation from the raw data files
r Responsiveness of warping. 0 will give a linear warp based on start and end points. 100 will use all bijective anchors
g Gap penalty given in comma separated string: initiate,extend (*)Defaults: (gap_init,gap_extend) [by score type]: 'cor' = '0.3,2.4' 'cov' = '0,11.7' 'prd' = '0,7.8' 'euc' = '0.9,1.8'
cor Score function: (*)cor (Pearson's R) or cor_opt (better runtime), cov (covariance), prd (product), euc (Euclidean distance)
l Local rather than *global alignment
i_ Penalty for initiating alignment (for local alignment only) (*)Default: 0

Value

An xcmsSet object

Methods

object = "xcmsSet"
retcor(object, method="obiwarp", plottype = c("none", "deviation", "mdevden"),col = NULL, ty = NULL, profStep=1, r=NULL, g=NULL, cor = NULL, l=NULL, i_=0)

See Also

xcmsSet-class,


[Package xcms version 1.16.3 Index]