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