createFSPY {flowSpy}R Documentation

create an FSPY object

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

}


[Package flowSpy version 1.0.4 Index]