gs_compare_cytobank_counts: compare the counts to cytobank's exported csv so that the...

In RGLab/CytoML: A GatingML Interface for Cross Platform Cytometry Data Sharing

compare the counts to cytobank's exported csv so that the parsing result can be verified.

Description

compare the counts to cytobank's exported csv so that the parsing result can be verified.

Usage

gs_compare_cytobank_counts(
  gs,
  file,
  id.vars = c("FCS Filename", "population"),
  ...
)

Arguments

gs	parsed GatingSet
file	the stats file (contains the populatio counts) exported from cytobank.
id.vars	either "population" or "FCS filename" that tells whether the stats file format is one population per row or FCS file per row.
...	arguments passed to data.table::fread function

Value

a data.table (in long format) that contains the counts from openCyto and Cytobank side by side.

Examples

acsfile <- system.file("extdata/cytobank_experiment.acs", package = "CytoML")
ce <- open_cytobank_experiment(acsfile)
gs <- cytobank_to_gatingset(ce)
## verify the stats are correct
statsfile <- ce$attachments[1]
dt_merged <- gs_compare_cytobank_counts(gs, statsfile, id.vars = "population", skip = "FCS Filename")
all.equal(dt_merged[, count.x], dt_merged[, count.y], tol = 5e-4)

RGLab/CytoML documentation built on Feb. 1, 2024, 12:34 a.m.