## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("NxtIRFdata") ## ----------------------------------------------------------------------------- library(NxtIRFdata) ## ----------------------------------------------------------------------------- example_fasta = chrZ_genome() example_gtf = chrZ_gtf() ## ----results = FALSE, message=FALSE------------------------------------------- bam_paths = example_bams(path = tempdir()) ## ----results = FALSE, message=FALSE------------------------------------------- # To get the MappabilityExclusion for hg38 as a GRanges object gr = get_mappability_exclusion(genome_type = "hg38", as_type = "GRanges") # To get the MappabilityExclusion for hg38 as a locally-copied gzipped BED file bed_path = get_mappability_exclusion(genome_type = "hg38", as_type = "bed.gz", path = tempdir()) # Other `genome_type` values include "hg19", "mm10", and "mm9" ## ----results = FALSE, message=FALSE------------------------------------------- library(ExperimentHub) ## ----eval = FALSE------------------------------------------------------------- # eh = ExperimentHub() # NxtIRF_hub = query(eh, "NxtIRF") # # NxtIRF_hub # # temp = eh[["EH6792"]] # temp # # temp = eh[["EH6787"]] # temp ## ----eval=FALSE--------------------------------------------------------------- # ?`NxtIRFdata-package` ## ----------------------------------------------------------------------------- sessionInfo()