homoPkgBuilder {AnnBuilder}R Documentation

Functions to build a homology data package using data from NCBI

Description

This function builds a data package that maps internal HomoloGene ids of an organism to LocusLink ids, UniGene ids, percent identity of the alignment, type of similarities, and url to the source of a curated orthology of organisms of all pairwise best matches based on data from ftp://ftp.ncbi.nih.gov/pub/HomoloGene/hmlg.ftp

Usage

homoPkgBuilder(suffix = "homology", pkgPath, version, author, url =
getSrcUrl("HG"))
procHomoData(url = getSrcUrl("HG"))
getLL2IntID(homoData, organism = "")
mapOrgs(toMap, what = c("code","name"))
mapPS(homoMappings, pkgName, pkgPath, tempList)
getHomoDList(data, what = "old")
getHomoData(entries, what = "old", objOK = FALSE)
getOrgNameNCode()
saveOrgNameNCode(pkgName, pkgPath, tepList)
HomoData2List(data, what = "old")

Arguments

suffix suffix a character string for the suffix to be attached to the end of a three-letter short form for an organism to form the name of a package to be created for homologous genes of the organism
pkgName pkgName a character string for the name of data package to be built
pkgPath pkgPath a character string for the name of the directory where the created package will be stored
version version a character string for the verion number of the package to be built
author author a list with an author element for the name of the author and a maintainer element for the name and e-mail address of the maintainer of the package
url url the url to the ftp site from which the source data file can be obtained. The default value is url{ftp://ftp.ncbi.nih.gov/pub/HomoloGene/hmlg.ftp}
homoData homoDatgetHomoDLista a data frame that contains the homology data from the source
homoMappings homoMappings same as homoData but only contains data for an organism of concern
organism organism a character string for the name of the organism of interest
toMap vect a vector of character strings
entries entries a vector of character strings
data data a data matrix
what what a character string that can either be "code" or "name" for function mapOrgs or "old" or "xml" for functions getHomoDList, getHomoData, and HomoData2List
tepList tepList a list containing key and value pairs that are going to be used to replace the corresponding matching items in a template file for man pages
tempList tempList same as tepList
objOK objOK a boolean indicating whether the homoDATA environment will be a list of homoDATA (TRUE) objects or lists (FALSE)

Details

procHomoData process the source data and put the data into a data frame that will be used later.

getLL2IntID maps LocusLink ids to HomoloGene internal ids

getIntIDMapping maps HomoloGene ids to ids include LocusLink ids, GneBank accession numbers, percent similarity values, type of similarities, and the url to the curated orthology.

mapIntID captures the reverse mapping between reciprocal homologous genes.

mapOrgs converts organism codes to scientific names.

writeRdaNMan creates an rda file and the corresponding man page for a data environment.

mapPS maps HomologGene Internal ids to homoPS objects generated using data from the source.

getHomoPS creates a homoPS object using data passed as a vector.

Value

procHomoData, mapIntID, and getLL2IntID returns a matrix.
getIntIDMapping returns an R environment with mappings between HomoloGene internal ids and mapped data.
getHomoPS returns a homoPS object with slots filled with data passed.
mapOrgs returns a vector of character strings.

Note

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

Author(s)

Jianhua Zhang

References

ftp://ftp.ncbi.nih.gov/pub/HomoloGene/README

See Also

ABPkgBuilder

Examples

# Examples are provided for only a few functions to avoid lengthy
# execution time


[Package AnnBuilder version 1.4.21 Index]