cqc_fix: Apply the cqc_solution

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

Apply the cqc_solution

Description

Peform the actual fixing action (i.e update or delete)

Usage

cqc_fix(x, ...)

Arguments

x	the cqc_solution returned by cqc_match calls
...	addiitional arguments not for the user.

Examples

# Read in FCS files with inconsistencies
fcs_files <- list.files(system.file("extdata", "GvHD_QC", package = "cytoqc"), full.names = TRUE)
qc_cf_list <- cqc_load_fcs(fcs_files)

# Check for marker inconsitencies
groups <- cqc_check(qc_cf_list, type = "marker")

# Attempt to fix them automatically
match_result <- cqc_match(groups, ref = c("CD14 PerCP", "CD15 FITC", "CD33 APC", "CD45 PE", "FSC-Height", "SSC-Height", "Time"))

# Add a manual match that automatic matching could not find
match_result <- cqc_match_update(match_result, map = c("PTPRC PE" = "CD45 PE"))

# Apply the fix to the original cytoframes
cqc_fix(match_result)

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