cqc_check: Perform a QC check on flow data.

In RGLab/cytoqc: Quality control and standardization of cytometry data

Perform a QC check on flow data.

Description

This is the first step of the entire qc workflow. It extracts meta information(specified by 'type' argument) from the raw data and compare/group them across samples. This provides a sample-wise data table for the further summary report.

Usage

cqc_check_channel(x, ...)

cqc_check_marker(x, ...)

cqc_check_panel(x, by = "channel", ...)

cqc_check_keyword(x, ...)

cqc_check_gate(x, ...)

cqc_check(x, ...)

Arguments

x	cqc_cf_list, cqc_gs, or cqc_gs_list object
...	additional arguments. type – specify the qc type, can be "channel", "marker" or "panel" delimiter – a special character used to separate channel and marker keys – The vector to supply the keys to be grouped on. default is NULL, which is extracted automatically from the flow data
by	the column used as the anchor when 'x' is the check result of panel, it can be either 'channel' or 'marker'

Value

a tibble with 4 columns: object, qc type (e.g. channel), group_id and nobject (i.e. group count)

Examples

fcs_files <- list.files(system.file("extdata", "GvHD_QC", package = "cytoqc"), full.names = TRUE)
qc_cf_list <- cqc_load_fcs(fcs_files)

# You may directly call the method for the parameter you would like to check
keyword_groups <- cqc_check_keyword(qc_cf_list)
keyword_groups

# Or use the type argument
channel_groups <- cqc_check(qc_cf_list, type = "channel")
channel_groups

panel_groups <- cqc_check(qc_cf_list, type = "panel", by = "marker")
panel_groups

RGLab/cytoqc documentation built on Jan. 25, 2023, 11:05 p.m.