How can i write as a csv file for S4 class?

Question

I am using DEP proteomics package to analyse my mass spectometry data. I want to remove the batch effect from the my data. So after the preprocessing of my data i want to download as a CSV file file so that i can upload into batch server. but I am not able to write as CSV. Whenever i try i am getting error (no method for coercing this S4 class to a vector)? I am new to R. i read something about this and still i don't have clear idea? can someone help me with this?

> data_se <- make_se(data_unique, LFQ_columns, experimental_design)

> LFQ_columns <- grep("LFQ.", colnames(data_unique))

> data_se_parsed <- make_se_parse(data_unique, LFQ_columns)

> is(data_se)

[1] "SummarizedExperiment" "RectangularData" "Vector" "Annotated"
[5] "vector_OR_Vector"

> data_se@metadata

list()

> View(data_se)

> colnames(data_se)

[1] "Ubi4_1" "Ubi4_2" "Ubi4_3" "Ubi6_1" "Ubi6_2" "Ubi6_3" "Ctrl_1" "Ctrl_2" "Ctrl_3" "Ubi1_1" "Ubi1_2" "Ubi1_3"

> write.csv2(data_se, "/home/dell/Desktop/Preoteomics_TMT_data/ubi_data_se.csv")

Error in as.vector(x) : no method for coercing this S4 class to a vector

Answer 1

Sorry, the question is not too clear (not sure what you want to upload for example), but you can access and write to file what looks like mass spec readings using the following:

my_data <- data_se@assays@data@listData
write.csv2(my_data, "my_upload.csv")

It probably won't be in the format needed for your batch server, but that is a separate question.

Not sure if this is the data you want! If you have no luck here, try biostars, where this type of question is more common.