## ----dependencies, warning=FALSE, message=FALSE---------------------------- library(mpra) ## -------------------------------------------------------------------------- E <- 4 # Number of elements B <- 3 # Number of barcodes s <- 4 # Samples per tissue nt <- 2 # Number of tissues set.seed(434) rna <- matrix(rpois(E*B*s*nt, lambda = 30), nrow = E*B, ncol = s*nt) dna <- matrix(rpois(E*B*s*nt, lambda = 30), nrow = E*B, ncol = s*nt) rn <- as.character(outer(paste0("barcode_", seq_len(B), "_"), paste0("elem_", seq_len(E)), FUN = "paste0")) cn <- c(paste0("liver_", seq_len(s)), paste0("kidney_", seq_len(s))) rownames(rna) <- rn rownames(dna) <- rn colnames(rna) <- cn colnames(dna) <- cn rna dna ## -------------------------------------------------------------------------- eid <- rep(paste0("elem_", seq_len(E)), each = B) eid ## -------------------------------------------------------------------------- eseq <- replicate(E, paste(sample(c("A", "T", "C", "G"), 10, replace = TRUE), collapse = "")) eseq <- rep(eseq, each = B) eseq ## -------------------------------------------------------------------------- mpraset_example <- MPRASet(DNA = dna, RNA = rna, eid = eid, eseq = eseq, barcode = NULL) mpraset_example ## -------------------------------------------------------------------------- E <- 4 # Number of elements B <- 3 # Number of barcodes s <- 4 # Total number of samples nalleles <- 2 # Number of alleles set.seed(434) rna <- matrix(rpois(E*B*s*nalleles, lambda = 30), nrow = E*B, ncol = s*nalleles) dna <- matrix(rpois(E*B*s*nalleles, lambda = 30), nrow = E*B, ncol = s*nalleles) rn <- as.character(outer(paste0("barcode_", seq_len(B), "_"), paste0("elem_", seq_len(E)), FUN = "paste0")) cn <- c(paste0("allele1_sample", seq_len(s)), paste0("allele2_sample", seq_len(s))) rownames(rna) <- rn rownames(dna) <- rn colnames(rna) <- cn colnames(dna) <- cn rna dna ## -------------------------------------------------------------------------- mpraset_example2 <- MPRASet(DNA = dna, RNA = rna, eid = eid, eseq = eseq, barcode = NULL) mpraset_example2 ## -------------------------------------------------------------------------- data(mpraSetExample) ## ---- fig=TRUE------------------------------------------------------------- design <- data.frame(intcpt = 1, episomal = grepl("MT", colnames(mpraSetExample))) mpralm_fit <- mpralm(object = mpraSetExample, design = design, aggregate = "mean", normalize = TRUE, model_type = "indep_groups", plot = TRUE) ## -------------------------------------------------------------------------- toptab <- topTable(mpralm_fit, coef = 2, number = Inf) toptab6 <- head(toptab) ## ----printToptab10--------------------------------------------------------- rownames(toptab6) rownames(toptab6) <- NULL toptab6 ## ----sessionInfo, results='asis', echo=FALSE------------------------------- sessionInfo()