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This is an quick start manual of BALLI
require(BALLI)
data <- data.frame(read.table("counts.txt"))
or make example count data
GenerateData <- function(nRow) { expr_mean <- runif(1,10,100) expr_size <- runif(1,1,10) expr <- rnbinom(20,mu=expr_mean,size=expr_size) return(expr) } data <- data.frame(t(sapply(1:10000,GenerateData))) colnames(data) <- c(paste0("A",1:10),paste0("B",1:10)) rownames(data) <- paste0("gene",1:10000) head(data)
Group <- c(rep("A",10),rep("B",10)) Group
design <- model.matrix(~Group, data = data) head(design)
dge <- DGEList(counts=data, group=Group) dge <- calcNormFactors(dge) dge
tV <- tecVarEstim(dge,design) tV
fit <- balli(tV,intV=2) fit
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