How to generate dataset like Bodenmiller_BCR_XL_SE()?
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larlay commented
would you show me an example?
i read "CyTOF workflow" doi: 10.12688/f1000research.11622.2, not same.
`
md <- "PBMC8_metadata.xlsx"
md <- read_excel(md)
head(data.frame(md))
panel <- "PBMC8_panel_v3.xlsx"
panel <- read_excel(panel)
head(data.frame(panel))
fcs_raw <- read.flowSet(md$file_name, transformation = FALSE, truncate_max_range = FALSE)
all(panel$fcs_colname %in% colnames(fcs_raw))
md$condition <- factor(md$condition, levels = c("Ref", "BCRXL"))
md$sample_id <- factor(md$sample_id, levels = md$sample_id[order(md$condition)])
sce <- prepData(fcs_raw, panel, md, features = panel$fcs_colname)`
larlay commented