scores: Returns a specified object from the cytofQC...

In jillbo1000/cytofQC: Labels normalized cells for CyTOF data and assigns probabilities for each label

Returns a specified object from the cytofQC SingleCellExperiment

Description

Returns a specified object from the cytofQC SingleCellExperiment

Usage

scores(x, type = c("all", "bead", "debris", "doublet", "dead"))

probs(x, type = c("all", "bead", "debris", "doublet", "dead"))

label(x)

tech(
  x,
  type = c("all", "Bead", "DNA", "Viability", "Event_length", "Center", "Offset",
    "Width", "Residual")
)

initial(x, type = c("all", "bead", "debris", "doublet", "dead"))

Arguments

x

A SingleCellExperiment created with readCytof with the scores and initial columns filled out for the event type of interest.

type

Identifies the type of objects to be returned. For scores and probs, type can be one or more of 'bead', 'dead', 'debris', or 'doublet'. For tech it can be any of the QC variables. It will return the numeric vector or DataFrame for the score(s) or probability for the specified event type(s). If the event types are not specified, the DataFrame containing all of the scores or all of the probability will be returned. This argument does nothing for label.

Value

For probs, scores, and tech, a numeric vector or DataFrame with the information for the event type(s) is returned.

For label, a character vector containing the label for each event is returned.

For tech, a DataFrame containing the technical variables used to determine the label of each event. The bead, DNA, and viability variables have an arcsinh transform, Event_length is unchanged, and the Gaussian parameters have a log transform using log1p.

Examples

data("raw_data", package = "CATALYST")
sce <- readCytof(raw_data, beads = "Beads", viability = c("cisPt1", "cisPt2"))
sce <- labelQC(sce)
table(label(sce))
cytofHist(scores(sce, type = 'bead'), label(sce), title = "Bead score")

jillbo1000/cytofQC documentation built on Aug. 23, 2023, 9:47 p.m.