Parameters for creation of extracted ion chromatograms.
getDefEICParams(...)To configure the creation of extracted ion chromatograms (EICs) several parameters exist:
rtWindow Retention time (in seconds) that will be subtracted/added to respectively the minimum and
maximum retention time of the feature. Thus, setting this value to >0 will 'zoom out' on the retention time
axis.
topMost Only create EICs for this number of top most intense features. If NULL then EICs are
created for all features.
topMostByRGroup If set to TRUE and topMost is set: only create EICs for the top most
features in each replicate group. For instance, when topMost=1 and topMostByRGroup=TRUE, then EICs will
be plotted for the most intense feature of each replicate group.
onlyPresent If TRUE then EICs are created only for analyses in which a feature was detected. If
onlyPresent=FALSE then EICs are generated for all analyses. The latter is handy to evaluate if a peak
was 'missed' during feature detection or removed during e.g. filtering.
if onlyPresent=FALSE then the following parameters are also relevant:
mzExpWindow To create EICs for analyses in which no feature was found, the m/z value is derived
from the min/max values of all features in the feature group. The value of mzExpWindow further expands this
window.
setsAdductPos,setsAdductNeg In sets workflows the adduct must be known to calculate the
ionized m/z. If a feature is completely absent in a particular set then it follows no adduct annotations are
available and the value of setsAdductPos (positive ionization data) or setsAdductNeg (negative
ionization data) will be used instead.
These parameters are passed as a named list as the EICParams argument to functions that use EICs. The
getDefEICParams function can be used to generate such parameter list with defaults.