createFSPY: create an FSPY object

In flowSpy: A Toolkit for Flow And Mass Cytometry Data

Description

This function is about how to build an FSPY object. An FSPY object is the base for the whole analysizing workflow of flow and mass cytometry data.

Usage

createFSPY(
  raw.data,
  markers,
  meta.data,
  batch = NULL,
  batch.correct = FALSE,
  normalization.method = "none",
  verbose = FALSE,
  ...
)

Arguments

raw.data	matrix. Raw data read from FCS file after perform preprocessing.
markers	vector. Detailed marker information in the gate of flow cytometer.
meta.data	data.frame. Raw metadata of each cell. Columns "cell" and "stage" are required.
batch	vector. Batch covariate (only one batch allowed). Method to correct batch effect function is refered to ComBat.
batch.correct	logical. Whether to correct batch effect. If TRUE, batch must be provided.
normalization.method	character. Normalization and transformation method. Whether to normalize and log transformed of raw.data. In flowSpy workflow, it's better to perform transformation of FCS data using runExprsExtract or runExprsMerge before creating an FSPY object. flowSpy only provide log transforma method. If you need to using truncateTransform, scaleTransform, linearTransform, quadraticTransform and lnTransform, see flowCore for more information. And runExprsExtract in flowSpy, autoLgcl, cytofAsinh, logicle, arcsinh, and logAbs can be used to perform transformation of FCS data.
verbose	logical. Whether to print calculation progress.
...	paramters pass to correctBatchFSPY function.

Value

An FSPY object with raw.data and markers and meta.data

Examples

if (FALSE) {
## See vignette tutorials
vignette(package = "flowSpy")
vignette("Quick_start", package = "flowSpy")

## Build using test data
markers <- c("CD43", "CD34", "CD90", "CD45RA",
             "CD31", "CD49f", "CD73", "FLK1", "CD38")

fspy <- createFSPY(raw.data = test.fcs.data,
                   markers = markers,
                   meta.data = test.meta.data,
                   normalization.method = "log",
                   verbose = TRUE)

fspy

}

flowSpy documentation built on Nov. 8, 2020, 6:53 p.m.