cytoqc – A QC tool for openCyto

cytoqc performs pre-cleaning, pre-gating and post-gating QC checks.

The alternative workflow:

Run cqc_group to see the summary
Manually provide the standard parameter names and cqc_find_solution for selected groups
cqc_fix based on the solution or cqc_drop_groups for unsolvable issues

library(flowCore)
library(flowWorkspace)
# library(cytoqc)
devtools::load_all("../")

Load the FCS

files <- list.files(data_dir, ".fcs", full.names = TRUE)
cqc_data <- cqc_load_fcs(files)
cqc_data

## cytoqc data: 
## 35  samples

QC for marker

#summarise marker groups
groups <- cqc_group(cqc_data, "marker")
su <- summary(groups)
knit_print(su)

group_id	nFCS	marker
3	21	CD14 PerCP, CD15 FITC, CD33 APC, CD45 PE, FSC-Height, SSC-Height, Time (102.40 sec.)
5	7	CD14 PerCP, CD15 FITC, CD33 APC, CD45 PE, FSC-Height, SSC-Height, Time (51.20 sec.)
4	5	CD14 PerCP, CD15 FITC, CD33 APC, CD45 PE, FSC-Height, SSC-Height, Time (204.80 sec.)
1	1	apc cd33, CD14 PerCP, cd15, CD45 PE, FSC-Height, SSC-Height, Time (102.40 sec.)
2	1	CD14 PerCP, CD15 FITC, CD33 APC, CD45 PE, FSC-Height, markerA, SSC-Height, Time (102.40 sec.)

Match against the references

res <- cqc_match_reference(groups, ref = c("cd15", "cd45", "cd14", "cd33"), select = 1:5)
solution <- cqc_find_solution(res, max.distance = 0.6) 
solution

Proposed change
CD45 PE –> cd45
apc cd33 –> cd33
CD14 PerCP –> cd14
FSC-Height
SSC-Height
Time (102.40 sec.)
CD33 APC –> cd33
CD15 FITC –> cd15
markerA
Time (204.80 sec.)
Time (51.20 sec.)

cqc_fix(solution)

update checks

groups <- cqc_group(cqc_data, "marker")
summary(groups)

group_id	nFCS	marker
1	35	cd14, cd15, cd33, cd45

A QC tool for openCyto 2

cytoqc – A QC tool for openCyto

The alternative workflow:

Load the FCS

QC for marker

Match against the references

update checks