do.align: do.align - Function to align multiple batches of a dataset.
In ImmuneDynamics/Spectre: High-dimensional cytometry and imaging analysis

do.align

R Documentation

do.align - Function to align multiple batches of a dataset.

Description

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.