## ----message=FALSE, warning=FALSE--------------------------------------------- library(sesameData) library(GenomicRanges) ## ----------------------------------------------------------------------------- head(sesameDataList()) ## ----include = FALSE---------------------------------------------------------- sesameDataCacheExample() # examples ## ----------------------------------------------------------------------------- sesameDataCache() ## ----------------------------------------------------------------------------- HM27.address <- sesameDataGet('HM27.address') ## ----------------------------------------------------------------------------- sesameDataGet_resetEnv() ## ----------------------------------------------------------------------------- txns_gr <- sesameData_getTxnGRanges("mm10") txns_gr ## ----------------------------------------------------------------------------- genes_gr <- sesameData_txnToGeneGRanges(txns_gr) genes_gr ## ----------------------------------------------------------------------------- probes <- names(sesameData_getManifestGRanges("Mammal40"))[1:500] head(probes) # our input txns <- sesameData_getTxnGRanges("hg38") pm <- promoters(txns, upstream = 1500, downstream = 1500) pm <- pm[pm$transcript_type == "protein_coding"] sesameData_annoProbes(probes, pm, column = "gene_name") ## ----------------------------------------------------------------------------- gr <- sesameData_getManifestGRanges("HM450") length(gr) ## ----message = FALSE, warning = FALSE----------------------------------------- library(GenomicRanges) ## ----------------------------------------------------------------------------- regs <- GRanges('chr5', IRanges(135313937, 135419936)) sesameData_getProbesByRegion(regs, platform = 'Mammal40') sesameData_getProbesByChromosome('chrX', platform = 'Mammal40') sesameData_getAutosomeProbes("Mammal40") sesameData_getProbesByGene('DNMT3A', "Mammal40", upstream=500) sesameData_getProbesByTSS('DNMT3A', "Mammal40") ## ----------------------------------------------------------------------------- TSSprobes = sesameData_getProbesByTSS(NULL, "Mammal40") ## ----------------------------------------------------------------------------- sesameData_getGenesByProbes(c("cg14620903","cg22464003"), max_distance = 10000) ## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("sesameData") ## ----eval=FALSE--------------------------------------------------------------- # BiocManager::install("zwdzwd/sesameData") ## ----------------------------------------------------------------------------- sessionInfo()