homoPkgBuilder {AnnBuilder} | R Documentation |
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
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")
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) |
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.
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.
The functions are part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities using R
Jianhua Zhang
ftp://ftp.ncbi.nih.gov/pub/HomoloGene/README