## ---- install, eval = FALSE--------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("getDEE2") ## ---- lib--------------------------------------------------------------------- library("getDEE2") ## ---- getmeta----------------------------------------------------------------- mdat <- getDEE2Metadata("celegans") head(mdat) ## ---- filtermeta-------------------------------------------------------------- mdat[which(mdat$SRP_accession %in% "SRP009256"),] ## ---- getSRRs----------------------------------------------------------------- mdat1 <- mdat[which(mdat$SRP_accession %in% "SRP009256"),] SRRvec <- as.vector(mdat1$SRR_accession) SRRvec ## ---- example1---------------------------------------------------------------- suppressPackageStartupMessages(library("SummarizedExperiment")) x <- getDEE2("celegans",SRRvec,metadata=mdat,counts="GeneCounts") x # show sample level metadata colData(x)[1:7] # show the counts head(assays(x)$counts) ## ---- testabsent-------------------------------------------------------------- x <- getDEE2("celegans",c("SRR363798","SRR363799","SRR3581689","SRR3581692"), metadata=mdat,counts="GeneCounts") ## ---- legacy------------------------------------------------------------------ x <- getDEE2("celegans",SRRvec,metadata=mdat,legacy=TRUE) names(x) head(x$GeneCounts) head(x$TxCounts) head(x$QcMx) head(x$GeneInfo) head(x$TxInfo) ## ----bundle1------------------------------------------------------------------ bundles <- list_bundles("athaliana") head(bundles) query_bundles(species="athaliana",query="SRP058781", col="SRP_accession",bundles=bundles) x <- getDEE2_bundle("athaliana", "SRP058781", col="SRP_accession",counts="GeneCounts") assays(x)$counts[1:6,1:4] ## ----bundle2------------------------------------------------------------------ x <- getDEE2_bundle("drerio", "GSE106677", col="GSE_accession",counts="GeneCounts") assays(x)$counts[1:6,1:4] ## ----sessioninfo,message=FALSE------------------------------------------------ sessionInfo()