annotation: annotation

In PavlidisLab/ermineR: Gene set analysis with multifunctionality assessment

annotation

Description

annotation

Usage

annotation(
  annotation,
  aspects = c("Molecular Function", "Cellular Component", "Biological Process")
)

Arguments

annotation

Annotation. A file path, a data.frame or a platform short name (eg. GPL127). If given a platform short name it will be downloaded from annotation repository of Pavlidis Lab (https://gemma.msl.ubc.ca/annots/). To get a list of available annotations, use listGemmaAnnotations. Note that if there is a file or folder with the same name as the platform name in the directory, that file will be read instead of getting a copy from Pavlidis Lab. If this file isn't a valid annotation file, the function will fail. If providing a custom annotation file, see makeAnnotation to do it from R or erminej.msl.ubc.ca/help/input-files/gene-annotations/ to do it manually. If you are providing a custom gene set, you can leave annotation as NULL

aspects

Character vector. Which Go aspects to include in the analysis. Can be in long form (eg. 'Molecular Function') or short form (eg. c('M','C','B'))

PavlidisLab/ermineR documentation built on Sept. 12, 2022, 7:10 p.m.