This function allows you to align multiple batches of a dataset, using either a "Quantile" approach, or using "CytoNorm"
Usage
do.align(ref.dat, target.dat, batch.col, align.cols, method, goal,
nQ, Qmin, Qmax, write.ref.fcs, write.target.fcs)
do.align(ref.dat, target.dat, batch.col, align.cols, method = "CytoNorm",
goal = "mean", nQ = 101, Qmin = 0.01, Qmax = 0.99, write.ref.fcs = TRUE,
write.target.fcs = TRUE, mem.ctrl = TRUE)Arguments
- ref.dat
NO DEFAULT. If using method = "CytoNorm", this must be a FlowSOM object created by Spectre::do.prep.fsom. If using "Quantiles", then this must be
- target.dat
NO DEFAULT. A data.table of data you wish to align
- batch.col
NO DEFAULT. Character, column that denotes batches
- align.cols
NO DEFAULT. Character, a vector of columns that you wish to align.
- method
DEFAULT = "CytoNorm". Character, can be "CytoNorm" or "Quantile".
- goal
DEFAULT = "Mean". For method = "CytoNorm". Character, the goal to align to. Can either be "mean", or can be the name of one of the batches (e.g. "Batch1").
- nQ
DEFAULT = 101. For method = "CytoNorm". Numeric, the number of quanitles to use.
- Qmin
DEFAULT = 0.01. For method = "Quantiles". Numeric, the minimum valus for the lower threshold.
- Qmax
DEFAULT = 0.99. For method = "Quantiles". Numeric, the maximum value for the upper threshold.
- write.ref.fcs
DEFAULT = TRUE. Logical, do you want a quick copy of the reference sample FCS files.
- write.target.fcs
DEFAULT = TRUE. Logical, do you want a quick copy of the ALIGNED target sample FCS files.
- mem.ctrl
DEFAULT = TRUE. Runs gc() (garbage collection) after a number of steps to free up memory that hasn't been released quickly enough.
References
Ashhurst, T. M., et al. (2019). https://www.ncbi.nlm.nih.gov/pubmed/31077106
Author
Thomas M Ashhurst, thomas.ashhurst@sydney.edu.au