QC for SDY 820
library(flowCore)
library(flowWorkspace)
# library(cytoqc)
devtools::load_all()
Load data
path <- "~/remote/fh/fast/gottardo_r/mike_working/flowcap3/"
files <- list.files(path, pattern = ".fcs", full.names = T)
set.seed(1)
files <- sample(files, 40)
cqc_data <- cqc_load_fcs(files, which.lines = 1)
Check channel
check_res <- cqc_check(cqc_data, "channel")
check_res
|
group_id
|
nFCS
|
channel
|
|
1
|
40
|
B515-A, B710-A, FSC-A, FSC-H, G560-A, G610-A, G660-A, G710-A, G780-A, R660-A, R710-A, R780-A, SSC-A, Time, V450-A, V545-A, V565-A, V585-A, V605-A, V655-A, V705-A, V800-A
|
Check marker
check_res <- cqc_check(cqc_data, "marker")
check_res
|
group_id
|
nFCS
|
marker
|
|
1
|
15
|
|
|
4
|
9
|
CCR7, CD107A, CD154, CD27, CD3, CD4, CD45RO, CD57, CD8, IFNG, IL2, TNFA, VIVID/CD14
|
|
2
|
6
|
107a, 154, 45ro, ccr7, cd27, cd3, cd4, cd57, cd8, ifng, il2, tnfa, vivid/14
|
|
3
|
4
|
107a, ccr7, cd154, cd27, cd3, cd4, cd45ro, cd57, cd8, ifng, il2, tnfa, vivid/14
|
|
6
|
4
|
CCR7, CD154, CD27, CD3, CD4, CD45RO, CD57, CD8, IFNG, IL2, TNFA, VIVIDCD14
|
|
5
|
2
|
ccr7, cd107a, cd154, cd27, cd4, cd45ro, cd57, cd8, d3, ifng, il2, tnfa, vivid/cd14
|
Match reference
match_res <- cqc_match(check_res, ref = 4, max.dist = 0.5)
match_res
Apply the match
cqc_fix(match_res)
cqc_check(cqc_data, "marker")
|
group_id
|
nFCS
|
marker
|
|
2
|
21
|
CCR7, CD107A, CD154, CD27, CD3, CD4, CD45RO, CD57, CD8, IFNG, IL2, TNFA, VIVID/CD14
|
|
1
|
15
|
|
|
3
|
4
|
CCR7, CD154, CD27, CD3, CD4, CD45RO, CD57, CD8, IFNG, IL2, TNFA, VIVID/CD14
|
Check panel
res <- cqc_check(cqc_data, "panel")
res
Use group 1 to standardize the rest
cqc_fix_panel(res, 2, by = "channel")
cqc_check(cqc_data, "panel")
check keywords
res <- cqc_check(cqc_data, "keyword")
res
|
group_id
|
nFCS
|
keyword
|
|
1
|
24
|
CYTNUM, EXPERIMENT NAME, FILENAME, GUID, ORIGINALGUID, PATIENT ID, PLATE ID, PLATE NAME, SAMPLE ID, transformation, TUBE NAME, WELL ID
|
|
2
|
16
|
CYTNUM, EXPERIMENT NAME, FILENAME, GUID, ORIGINALGUID, PLATE ID, PLATE NAME, transformation, TUBE NAME, WELL ID
|
res <- cqc_match(res, ref = 1)
res
Merge the standarized data
cs <- cytoset(cqc_data)
cs
## A cytoset with 40 samples.
##
## column names:
## FSC-A, FSC-H, SSC-A, B710-A, B515-A, G780-A, G710-A, G660-A, G610-A, G560-A, R780-A, R710-A, R660-A, V800-A, V705-A, V655-A, V605-A, V585-A, V565-A, V545-A, V450-A, Time