Entering edit mode
I am using the flow cytometry quality control package cytocq for prosessing a large number of fcs files: How do I combine mulltiple cqc_data objects into one list of cytoframes/cqc_cf_list for further #analyses in the cytoqc pipeline?
library(flowCore)
library(flowWorkspace)
library(cytoqc)
#Load the FCS
files <- list.files(data_dir, ".fcs", full.names = TRUE)
cqc_data <- cqc_load_fcs(files)
cqc_data
## cytoqc data:
## 21 samples
#However:
cqc_data_1 <- cqc_load_fcs(files[1:3])
cqc_data_2 <- cqc_load_fcs(files[4:6])
cqc_data_3 <- cqc_load_fcs(files[7:21])
#How do I combine the lists cqc_data_1, cqc_data_2, cqc_data_3 into one list of cytoframes/cqc_cf_list for further analyses in the cytoqc pipeline?
Unless
cqc_datais simply a list, I don't think there is a quick answer if you haven't found it yet.I don't understand your approach.
cqc_datagot all the results in one place. Why did you decide to split the analysis, which requires to combine the results afterwards?Hi,
The object cqc_data is a 'cqc_cf_list', actually a list of cytoframes, if I understand correctly.
I have > 1500 fcs files, and have to split the task in several steps, to avoid errors. Thus, I load a subset of the files, and repeat this several times, resulting in approximately 10 cqc_data objects, and I want to combine these objects in the end.
OK. If in the end your process write the resulting FCS to the disk to perform the next step of the analysis, I don't feel the need to have a single
cqc_dataobject.You should post an issue at https://github.com/RGLab/cytoqc/issues to ensure Mike or Greg catch your question.
If you encounter errors, that will be helpful to report them on the github repo.