A collection of miscellanious R functions usefull to me. Currently included:
- gettairid, a function to extract the first Arabidopsis gene ID from a character string (following the TAIR nomenclature). The function also allowes for the selection of specific chromosomes or plastids. Since this function does not return a list it is more suitable for dataframe operations.
- gettairid_all, a function to extract Arabidopsis gene ID's from a character string (following the TAIR nomenclature). The function also allowes for the selection of specific chromosomes or plastids. Since this function returns a list of all geneid's in the query string it is more suitable for text extraction.
- goseq_nm, a function performing Gene Ontology enrichment for non-model species.
- get_peaks a function to extract peaks from Malley et al 2016 (doi: 10.1016/j.cell.2016.04.038) of a given (promotor) section of interest.
- get_tf_from_peaks to get unique geneids from transcription factors binding in given promotor section.
You are welcome to use them!
To install the package please run:
install.packages("devtools")
devtools::install_github("KTMD-plant/gaRdenbox")