Combines two massSight objects, resulting in a single
MergedMSObject.
Usage
auto_combine(
ms1,
ms2,
rt_lower = -0.5,
rt_upper = 0.5,
mz_lower = -15,
mz_upper = 15,
minimum_intensity = 10,
iso_method = "manual",
eps = 0.1,
rt_iso_threshold = 0.1,
mz_iso_threshold = 5,
match_method = "unsupervised",
smooth_method = "gam",
weights = c(1, 1, 1),
log = NULL,
output = NULL
)Arguments
- ms1
A
massSightobject representing the results of a preprocessed LC-MS experiment.- ms2
A
massSightobject representing the results of a second preprocessed LC-MS experiment.- rt_lower
A numeric indicating the lower bound of the RT range to be considered for aligning two metabolites.
- rt_upper
A numeric indicating the upper bound of the RT range to be considered for aligning two metabolites.
- mz_lower
A numeric indicating the lower bound of the m/z range to be considered for aligning two metabolites.
- mz_upper
A numeric indicating the upper bound of the m/z range to be considered for aligning two metabolites.
- minimum_intensity
A numeric indicating the minimum intensity to be considered for alignment.
- iso_method
The isolation method used before modeling drift. Can either be "manual" or "dbscan".
- eps
Epsilon value for dbscan algorithm. Only used if iso_method = "dbscan"
- rt_iso_threshold
A numeric indicating the isolation parameter for RT.
- mz_iso_threshold
A numeric indicating the isolation parameter for m/z.
- match_method
A character indicating the initial matching method to be used to detect inter-batch variability. Options are "unsupervised" and "supervised".
- smooth_method
A character indicating the smoothing method to be used. Options are "lowess", "spline", and "gaussian".
- weights
A numeric vector indicating the weights to be used for the alignment.
- log
A character indicating the name of the log file.
- output
A character indicating the directory to save the output. If NULL, the output will be saved in the current working directory.