basicAnno: Basic gene annotation

In frankRuehle/systemsbio: Streamlined Analysis and Integration of Systems Biology Data

Description

Annotate gene symbols and EntrezIDs using an organism-specific annotation package.

Usage

basicAnno(
  data,
  Symbol.column = "SYMBOL",
  Entrez.column = "ENTREZID",
  org = "human"
)

Arguments

data	dataframe or character with filepath to data to be loaded.
Symbol.column	character with column name of Gene Symbols in data. if NULL, SYMBOLs are derived from Entrez.column using the annotation package for org.
Entrez.column	character with column name of ENTREZ IDs in data. if NULL, ENTREZ IDs are derived from Symbol.column using the annotation package for org. Either Symbol.column or Entrez.column must be specified.
org	character with species name ("human", "mouse", "rat").

Details

This function adds annotation of either gene SYMBOL or ENTREZID to data using the corresponding annotation package of the organism specified in org. and the join-function of the plyr package. Order of input object is not changed. No additional rows introduced.

Value

dataframe with added annotation column (either SYMBOL or ENTREZID).

Author(s)

Frank Ruehle

frankRuehle/systemsbio documentation built on Sept. 14, 2020, 1:18 a.m.