SAGEMapper {SAGElyzer} | R Documentation |
Functions that provide data annotation using public databases and package AnnBuilder
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()
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 |
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
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 |
The functions are part of the Bioconductor project at Dana-Farber Cancer Institute to provide bioinformatics functionalities through R
J. Zhang
The help files for package AnnBuilder provides explations on how to annotate data using AnnBuilder
# 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)