gs_compare_cytobank_counts {CytoML} | R Documentation

## 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)

[Package CytoML version 2.0.5 Index]