mirnaCounts.Rd
This function executes the docker container mrna8, which allows miRNAs counting.
mirnaCounts( group = c("sudo", "docker"), fastq.folder = getwd(), scratch.folder = "/data/scratch", mirbase.id = c("hsa", "mmu"), download.status = FALSE, adapter.type = c("ILLUMINA", "NEB"), trimmed.fastq = FALSE )
group, | a character string. Two options: |
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fastq.folder, | a character string indicating where mirna fastq are located |
scratch.folder, | a character string indicating the scratch folder where docker container will be mounted |
mirbase.id, | a character string indicating the mirbase prefix for the organism of interest, e.g. hsa for human or mmu for mouse |
download.status, | a boolean logical variable indicating if the latest mirbase database will be downloaded or the local mirbase 21 will be used. Default is FALSE |
adapter.type, | a character string. Two options: |
trimmed.fastq, | a boolean logical variable indicating if trimmed fastq are saved. Default is FALSE |
one file: annotated_genes.results, which is the annotated version of gene.results.
if (FALSE) { system("wget 130.192.119.59/public/test.mirnaCounts.zip") unzip("test.mirnaCounts.zip") setwd("test.mirnaCounts") library(docker4seq) mirnaCounts(group="docker",fastq.folder=getwd(), scratch.folder="/data/scratch", mirbase.id="hsa",download.status=FALSE, adapter.type="NEB", trimmed.fastq=FALSE) }