Description Usage Arguments Value Examples
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.
1 2 3 4 5 6 7 8 9 10 11 | 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, ...)
|
x |
|
... |
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' |
a tibble with 4 columns: object, qc type (e.g. channel), group_id and nobject (i.e. group count)
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.