An S4 class to represent the base information used by the methods.

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Description

An S4 class to represent the base information used by the methods.

Slots

db

A character string stating the NIH/NCBI database to be queried. (Default - "gene")

nihbase

A character string stating the base URL for NIH/NCBI queries.

ids

A Vector of character strings

uniprotbase

A character string stating the base URL for Uniprot queries.

uniprotquery

A character string stating additional information to optimize the query to the Uniport database.

uniprotcolumns

A character string stating the database columns to be returned from the Uniport database.

genelist

A vector of character strings representing a unique list of the genes queried.

fileroot

A charcter string of the directory for file input and storage. (defaults to working directory)

outputstem

A character string stating the sub-directory of 'fileroot' into which output files are saved. (Default - "gene_annotations")

genefilestem

A character string stating the sub-directory of 'fileroot' into which gene objects are saved. (Default - "genes")

groupnos

A numeric vector representing the identifiers of groups in the input file/list.