rsemanno: Annotating RSEM gene.results using ENSEMBL annotation

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

Annotating RSEM gene.results using ENSEMBL annotation

Description

This function executes the docker container annotate.1, where Bioconductor is used to annotated gene.results output of RSEM using ENSEMBL annotation

Usage

rsemanno(
  group = c("sudo", "docker"),
  rsem.folder = getwd(),
  scratch.folder = "/data/scratch",
  org = c("hg19", "hg38", "mm10", "mm9"),
  truncating.expected.counts = FALSE,
  protein.anno = FALSE
)

Arguments

group	a character string. Two options: "sudo" or "docker", depending to which group the user belongs
rsem.folder	a character string indicating where gene.results and isoforms.results are located
scratch.folder	a character string indicating the scratch folder where docker container will be mounted
org	a character string indicating the genome assembly used for mapping and counting with "rsemstar" function
truncating.expected.counts	a boolean logical variable indicating if the expected counts calculated by RSEM need to be converted in integer to be compliant with differnetial expression Bioconductor packages as DESeq2. Default is FALSE
protein.anno	a boolean logical variable indicating if instead of gene SYMBOL SWISSPROT symbol are used. This option is useful for integrating transcriptomics data with proteomics data

Value

one file: annotated_genes.results, which is the annotated version of gene.results.

Examples

## Not run: 
    #downloading fastq files
    system("wget http://130.192.119.59/public/genes.results.gz")
    gzip -d genes.results.gz
    #running rsemanno
    rsemanno(group="docker",rsem.folder=getwd(), scratch.folder="/data/scratch",
    org="hg38", truncating.expected.counts=FALSE,
    protein.anno=FALSE)


## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.