Hello everyone! I am working with the https://github.com/adamjamesreid/Plasmodium-single-cell-RNA-seq files. The first lines of the code are:
molecules <- read.table("PbM_counts.txt", sep = "\t", header = TRUE, row.names=1)
anno <- read.table("PbM_meta.txt", sep = "\t", header=TRUE)
genes <- read.table("berg.desc", header=FALSE, row.names=1, quote = "", sep="\t")
pheno_data <- new("AnnotatedDataFrame", anno)
rownames(pheno_data) <- pheno_data$sample_id
PbM <- SingleCellExperiment(assays = list(counts = as.matrix(molecules)),
colData = anno)
PbM$phenoData<- pheno_data
Now I need to deconvolute those data using bseq-sc package (https://shenorrlab.github.io/bseqsc/vignettes/bseq-sc.html). The first problem I have found is when I want to run the plotCellTotals with my data. This last command requires an ExpressionSet object, while my PbM is a SingleCellExperiment object. How can I make it work?