rsemanno.Rd
This function executes the docker container annotate.1, where Bioconductor is used to annotated gene.results output of RSEM using ENSEMBL annotation
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 )
group, | a character string. Two options: |
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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 |
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 |
one file: annotated_genes.results, which is the annotated version of gene.results.