annotateFlowSet: Annotate a flowSet with experimental metadata

In wrightrc/flowTime: Annotation and analysis of biological dynamical systems using flow cytometry

Annotate a flowSet with experimental metadata

Description

Add annotations to a flowSets phenoData and plate numbers, strain names, and treatment also set T0

Usage

annotateFlowSet(yourFlowSet, annotation_df, mergeBy = "name")

Arguments

yourFlowSet	a flowSet with sampleNames of the format 'plate#_Well', we typically use the following code chunk to read data from individual plates as exported from BD Accuri C6 software.
annotation_df	A data frame with columns 'well', 'strain', 'treatment', containing all of the wells in the flowset labeled with the strain and treatment in that well.
mergeBy	the unique identifier column

Value

An annotated flowSet

Examples

dat <- read.flowSet(path = system.file("extdata", "ss_example",
package = "flowTime"), alter.names = TRUE)
annotation <- read.csv(system.file("extdata", "ss_example.csv", package =
"flowTime"))
annotateFlowSet(dat, annotation, mergeBy = "name")

wrightrc/flowTime documentation built on Dec. 8, 2022, 9:50 p.m.