getAnnotationTable: A function that creates an Annotation table for microorrays...

In mssm-msf-2019/BiostatsALL:

Description

A function that creates an Annotation table for microorrays experiments. It must be associated with an existing Array annotation data (ie hgu133plus2.db) where annotations has been assembled using data from public repositories

this function annotates probeids by using AnnotationDbi package

Usage

getAnnotationTable(IDS, AnnPkg, w.annot = c("ENTREZID", "SYMBOL", "GENENAME",
  "OMIM", "CHRLOC", "PATH", "GO"), w.annot.unique = c("ENTREZID", "SYMBOL",
  "OMIM", "CHRLOC"))

getAnnotationTable(IDS, AnnPkg, w.annot = c("ENTREZID", "SYMBOL", "GENENAME",
  "OMIM", "CHRLOC", "PATH", "GO"), w.annot.unique = c("ENTREZID", "SYMBOL",
  "OMIM", "CHRLOC"))

Arguments

IDS	identification for the probesets
AnnPkg	annotation package (e.g. hgu133plus2.db)
IDS:	type of methods. Options are Regression, Classification adn Dual use
AnnPkg:	named of the Array annotation data (ie, hgu133plus2.db)
w.annot:	name of the information to be included in the table
w.annot.unique:	which columns should be used to solved duplicated annotation; ie when a probe have two gene names.
w.annot:	which information should be annotated
w.annot.unique:	unique annotation to be done

Examples

library(hgu133plus2.db)
AnnPkg <- hgu133plus2.db
getAnnotationTable(IDS=featureNames(eset), AnnPkg, w.annot=c("ENTREZID","SYMBOL","GENENAME"),w.annot.unique=c("ENTREZID"))
getAnnotationTable<-function(IDS, hgu133plus2.db, w.annot=c("ENTREZID","SYMBOL","GENENAME","OMIM","CHRLOC","PATH","GO"),w.annot.unique=c("ENTREZID","SYMBOL","OMIM","CHRLOC"))

mssm-msf-2019/BiostatsALL documentation built on May 22, 2019, 12:16 p.m.