I am trying to download bigwig files for each sample of RNA-Seq data in GTEx via recount2. I can see bigwig file names defined for each sample (probably for each gene) in the 19th column through the following command. Then, how can I download the actual bigwig files in the column?
> download_study("SRP012682", type = "rse-gene") > load(file.path("SRP012682", "rse_gene.Rdata")) > colnames(colData(rse_gene))
Actually, the recount Bioconductor vignette stated that downloadstudy can be set with type="samples" that returns one bigWig file per sample in the study. However, downloadstudy cannot recognize this parameter value. In either way, can you please help me to download GTEx RNA-Seq bigwig files for each sample?
> url <- download_study('SRP012682', type=samples) Error in type %in% c("rse-gene", "rse-exon", "rse-jx", "rse-tx", "counts-gene", : 'match' requires vector arguments