SAGEMapper {SAGElyzer}R Documentation

Annotating SAGE tags using data from public databases

Description

Functions that provide data annotation using public databases and package AnnBuilder

Usage

SAGEMapper(tag2UG = TRUE, tagUrl =
                 "ftp://ftp.ncbi.nih.gov/pub/sage/map/Hs/NlaIII/SAGEmap_tag_ug-rel.zip",
                 organism = "Hs", fromWeb = TRUE)
doTag2UG(fileName)
doUG2Tag(fileName, sep = "\t", header = FALSE)
getMapFileName()

Arguments

tag2UG A boolean set to be TRUE if the mapping will be between SAGE tags and UniGene ids or FALSE is the mapping will be between UniGene ids and SAGE tags
tagUrl A character string for the url where mapping information can be downloaded
fileName A character string for the name of the file where the mapping will be stored
sep sep a character string for the separator used in the source file
header header a boolean indicating whether the source file has a header line
organism organism a character string for the organism of concern (e. g. Hs for human)
fromWeb fromWeb a boolean indicating whether the source data should be downloaded from the web or read from a directory locally

Details

SAGEMapper reads mapping data from NCBI (ftp://ftp.ncbi.nih.gov/pub/sage/map/Hs/NlaIII/SAGEmap_tag_ug-rel_Hs.zip) and produces a text file containing the mappings between SAGE tags and UniGene ids or UniGene ids and SAGE tags. The default url was valid for human genes at the time of development but needs to be updated when needed.

doTag2UG, doUG2Tag, and env2File are called by SAGEMapper to perfome the required functions

Value

doTag2UG Returns an R environment object containing mappings between SAGE tags and UniGene ids
doUG2Tag Returns an R environment object containing mappings between UniGene ids SAGE tags

Note

The functions are part of the Bioconductor project at Dana-Farber Cancer Institute to provide bioinformatics functionalities through R

Author(s)

J. Zhang

References

The help files for package AnnBuilder provides explations on how to annotate data using AnnBuilder

See Also

SAGELyzer

Examples

# The following code takes a while to run and is thus inactivated
## Not run: 
SAGEMapper("theMap", "", TRUE,
"ftp://ftp.ncbi.nih.gov/pub/sage/map/Hs/NlaIII/SAGEmap_tag_ug-rel_Hs.zip")
## End(Not run)

[Package SAGElyzer version 1.4.2 Index]