## ----Load libraries, message=FALSE, warning = FALSE--------------------------- library(MultiDataSet) library(brgedata) library(GenomicRanges) ## ----New Multi---------------------------------------------------------------- multi <- createMultiDataSet() multi ## ----Names empty Multi-------------------------------------------------------- names(multi) length(names(multi)) ## ----add_eset 10-------------------------------------------------------------- data("brge_gexp") brge_gexp multi2 <- add_eset(multi, brge_gexp, dataset.type = "expression") multi2 multi ## ----add_eset 2--------------------------------------------------------------- multi2 <- add_eset(multi2, brge_gexp, dataset.type = "expression", dataset.name = "new") multi2 ## ----add_eset add id to eset-------------------------------------------------- brge_gexp2 <- brge_gexp brge_gexp2$id <- 1:100 multi2 <- add_eset(multi, brge_gexp2, dataset.type = "expression") multi2 ## ----add_eset overwrite, error=TRUE------------------------------------------- brge_gexp2 <- brge_gexp[, 1:10] multi2 <- add_eset(multi, brge_gexp, dataset.type = "expression", warnings = FALSE) multi2 multi2 <- add_eset(multi2, brge_gexp2, dataset.type = "expression", warnings = FALSE, overwrite = FALSE) multi2 multi2 <- add_eset(multi2, brge_gexp2, dataset.type = "expression", warnings = FALSE, overwrite = TRUE) multi2 ## ----add_eset GRanges--------------------------------------------------------- multi2 <- add_eset(multi, brge_gexp, dataset.type = "expression", warnings = FALSE, GRanges = NA) multi2 ## ----add_rse overwrite-------------------------------------------------------- data("brge_methy") brge_methy2 <- brge_methy[1:100, ] ### Subset the original set to speed up multi <- createMultiDataSet() multi2 <- add_rse(multi, brge_methy, dataset.type = "methylation", warnings = FALSE) multi2 ## ----add genexep-------------------------------------------------------------- multi <- createMultiDataSet() multi2 <- add_genexp(multi, brge_gexp) brge_gexp ## ----add genexp--------------------------------------------------------------- multi2 <- add_genexp(multi2, brge_gexp, dataset.name = "2") multi2 ## ----Subsetting intro--------------------------------------------------------- multi <- createMultiDataSet() # Remove probes without a position before adding the object multi <- add_methy(multi, brge_methy) multi <- add_genexp(multi, brge_gexp) multi <- add_eset(multi, brge_gexp, dataset.type = "test", GRanges = NA) multi ## ----subset samples----------------------------------------------------------- samples <- sampleNames(brge_gexp)[76:100] multi[samples, ] ## ----subset common samples---------------------------------------------------- commonSamples(multi) length(intersect(sampleNames(brge_gexp), sampleNames(brge_methy))) ## ----subset tables------------------------------------------------------------ multi[, "expression"] multi[, c("methylation", "test")] ## ----select tables------------------------------------------------------------ multi[["expression"]] multi[, "expression", drop = TRUE] ## ----Genomic Ranges----------------------------------------------------------- range <- GRanges("chr17:1-100000") multi[, , range] ## ----Genomic Ranges 2--------------------------------------------------------- range2 <- GRanges(c("chr17:1-100000", "chr17:1000000-2000000")) multi[, , range2] ## ----combined----------------------------------------------------------------- multi[samples, "expression", range] multi[samples, "methylation", range, drop = TRUE] ## ----Advanced genes----------------------------------------------------------- subset(multi, genes == "SLC35E2") ## ----Advanced genes 2--------------------------------------------------------- subset(multi, genes %in% c("SLC35E2", "IPO13", "TRPV1")) subset(multi, genes == "EEF1A1" | genes == "LPP") ## ----Advanced pheno----------------------------------------------------------- subset(multi, , sex == "Female") ## ----Combined advanced-------------------------------------------------------- subset(multi, genes == "SLC35E2", sex == "Female")