Anyone have used liger library for batch correction?

Hi,

I am quite new with this library and try to do batch correction using integrative non-negative matrix factorization (NMF).

I have problem when implementing the last part of this:

ari$tech <- plyr::mapvalues(ari$tech, from = c("celseq", "celseq2", "fluidigmc1", "smartseq2"), to = c(0, 1, 2, 3))

The error says:
The following from values were not present in x: celseq, celseq2, fluidigmc1, smartseq2

I think it's the splitting problem, but i am not sure.

My full script here:

tech <- unlist(lapply(1:length(data.liger@H), function(x) {
rep(names(data.liger@H), nrow(data.liger@H[]))}))
clusters <- data.liger@alignment.clusters
ari <- data.frame("tech" = tech, "clusters" = clusters)

ari$tech <- plyr::mapvalues(ari$tech, from = c("celseq", "celseq2", "fluidigmc1",
"smartseq2"), to = c(0, 1, 2, 3))

The full documentation is here: 12 Batch Correction Lab | ANALYSIS OF SINGLE CELL RNA-SEQ DATA

Thank you!

Best
IS

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