I have been trying to run the pcpr2 package using the following tutorial: https://github.com/JoeRothwell/pcpr2
The data for this package is available in this link: https://github.com/JoeRothwell/pcpr2/raw/master/data/PCPR2data.RData
My datamatrix file is: https://drive.google.com/file/d/1wzzw2Jcui-IKICYc_QmTCvXqeFZ_3teX/view?usp=share_link
My metadata file is: https://drive.google.com/file/d/1d52Cj4qNvjTJox7n5uZKlmF9d8YPpfAn/view?usp=share_link
My code:
transcripts <- read.csv("test_matrix.csv", row.names = 1)
Z_metadata <- read.csv("test_trait.csv")
output <- runPCPR2(transcripts , Z_metadata, pct.threshold = 0.8)
Each time I try to use my data to run the codes from the pcpr2 package, I get the following error:
Error in runPCPR2(transcripts, Z_metadata, pct.threshold = 0.8) :
is.numeric(X_DataMatrix) is not TRUE
I tried converting my datamatrix into a numeric format by the following command:
transcripts = lapply(transcripts , as.double)
transcripts = do.call("cbind", transcripts)
However, this didn't work also. I get another error message:
Error in solve.default(crossprod(model.matrix(mod))) :
Lapack routine dgesv: system is exactly singular: U[15,15] = 0
I can tell something is wrong with my datamatrix format as the datatype and the class ain't the same as the ones used in the tutorial. However, I don't understand how to fix this. Any sort of help will be greatly appriciated.
Be careful when importing the test_matrix dataset (there are rownames and it should be a matrix) :
transcripts=as.matrix(read.csv("https://raw.githubusercontent.com/dtonmoy/PCPR2-data/main/test_matrix.csv",row.names=1))
Z_metadata=read.csv("https://raw.githubusercontent.com/dtonmoy/PCPR2-data/main/test_trait.csv")
output <- runPCPR2(transcripts , Z_metadata, pct.threshold = 0.8)