rsemanno: Annotating RSEM gene.results using ENSEMBL annotation

Description Usage Arguments Value Examples

View source: R/rsemAnnotate.R

Description

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

Usage

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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

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## 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 Nov. 18, 2018, 11:12 a.m.