R/map_genes.R
In jlaffy/scalop: Single Cell Analysis Operations
Defines functions
x2y
map_genes
which_annotation
is_annotation
get_genes
Documented in
get_genes
is_annotation
map_genes
which_annotation
x2y
### retrieve all genes/entries for a particular annotation type ###
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keytype PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname get_genes
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
get_genes = function(keytype) {
.genes = function() {
org = Homo.sapiens::Homo.sapiens
AnnotationDbi::keys(org, keytype=keytype)
}
}
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname get_ucsc
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
get_ucsc=get_genes('UCSCKG')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname get_refseq
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
get_refseq=get_genes('REFSEQ')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname get_symbols
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
get_symbols=get_genes('SYMBOL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname get_ensembl
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
get_ensembl=get_genes('ENSEMBL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname get_entrez
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
get_entrez=get_genes('ENTREZID')
### return annotation type ###
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keytype PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname is_annotation
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
is_annotation = function(keytype) {
.is_annotation = function(keys) {
org = Homo.sapiens::Homo.sapiens
universe = AnnotationDbi::keys(org, keytype=keytype)
keys %in% universe
}
}
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname is_symbol
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
is_symbol = is_annotation('SYMBOL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname is_entrez
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
is_entrez = is_annotation('ENTREZID')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname is_ensembl
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
is_ensembl = is_annotation('ENSEMBL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname is_refseq
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
is_refseq = is_annotation('REFSEQ')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname is_accnum
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
is_accnum = is_annotation('ACCNUM')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname is_alias
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
is_alias = is_annotation('ALIAS')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname is_ucsc
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
is_ucsc = is_annotation('UCSCKG')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION
#' @param aliasesBeforeSymbols PARAM_DESCRIPTION, Default: FALSE
#' @param priority PARAM_DESCRIPTION, Default: NULL
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @rdname which_annotation
#' @export
which_annotation = function(keys, aliasesBeforeSymbols=FALSE, priority=NULL) {
keytypes = c('SYMBOL',
'ALIAS',
'ENTREZID',
'ENSEMBL',
'REFSEQ',
'ACCNUM',
'UCSCKG',
'TXID',
'ENSEMBLTRANS',
'ENSEMBLPROT',
'UNIPROT',
'UNIGENE',
'EXONID',
'ENZYME')
if (aliasesBeforeSymbols) {
if (!is.null(priority) && priority!='SYMBOL') keytypes[1:2] <- keytypes[2:1]
else message("You set priority to 'SYMBOL' so aliasesBeforeSymbols will be ignored.")
}
if (!is.null(priority)) {
if (!priority %in% keytypes) stop(priority, ' does not exist')
else keytypes = c(priority, setdiff(keytypes,priority))
}
.call = function(keytype) {
if (any(is.na(nams))) {nams[is.na(nams) & is_annotation(keytype)(keys)] <<- keytype}
}
nams = rep(NA,length(keys))
sapply(keytypes, .call)
setNames(nams, keys)
}
### map genes from one annotation type to others and return DF ###
### default return columns: SYMBOL, ENTREZID, TXCHROM ###
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keytype PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname map_genes
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys select
map_genes = function(keytype) {
.map_genes = function(keys=NULL, columns=NULL, add.columns=NULL, remove.columns=NULL) {
org = Homo.sapiens::Homo.sapiens
if (is.null(columns)) columns = c('SYMBOL','ENTREZID','TXCHROM')
columns = setdiff(columns,keytype)
columns = setdiff(columns,remove.columns)
columns = union(columns,add.columns)
if (is.null(keys)) {
keys = AnnotationDbi::keys(org, keytype=keytype)
}
AnnotationDbi::select(org,keys=keys,keytype=keytype,columns=columns)
}
}
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param columns PARAM_DESCRIPTION, Default: NULL
#' @param add.columns PARAM_DESCRIPTION, Default: NULL
#' @param remove.columns PARAM_DESCRIPTION, Default: NULL
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname map_entrez
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys select
map_entrez = map_genes('ENTREZID')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param columns PARAM_DESCRIPTION, Default: NULL
#' @param add.columns PARAM_DESCRIPTION, Default: NULL
#' @param remove.columns PARAM_DESCRIPTION, Default: NULL
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname map_symbol
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys select
map_symbol = map_genes('SYMBOL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param columns PARAM_DESCRIPTION, Default: NULL
#' @param add.columns PARAM_DESCRIPTION, Default: NULL
#' @param remove.columns PARAM_DESCRIPTION, Default: NULL
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname map_ensembl
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys select
map_ensembl = map_genes('ENSEMBL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param columns PARAM_DESCRIPTION, Default: NULL
#' @param add.columns PARAM_DESCRIPTION, Default: NULL
#' @param remove.columns PARAM_DESCRIPTION, Default: NULL
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname map_refseq
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys select
map_refseq = map_genes('REFSEQ')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param columns PARAM_DESCRIPTION, Default: NULL
#' @param add.columns PARAM_DESCRIPTION, Default: NULL
#' @param remove.columns PARAM_DESCRIPTION, Default: NULL
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname map_alias
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys select
map_alias = map_genes('ALIAS')
### convert between two keytypes ###
### this I think passes through ENTREZID ###
### if multiVals ='first', returns smallest ENTREZID
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param x PARAM_DESCRIPTION
#' @param y PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname x2y
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
x2y = function(x,y) {
.x2y = function(keys=NULL,multiVals='first') {
if (is.null(keys)) {
keys = get_genes(x)()
}
org = Homo.sapiens::Homo.sapiens
out=rep(NA,length(keys))
is.ready = is_annotation(y)(keys)
out[is.ready] <- keys[is.ready]
bool=!is.ready & is_annotation(x)(keys)
if (any(bool)) {
out[bool]<-AnnotationDbi::mapIds(org,
keys=keys[bool],
keytype=x,
column=y,
multiVals=multiVals)
}
out
}
}
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname alias2symbol
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
alias2symbol = x2y('ALIAS','SYMBOL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname alias2entrez
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
alias2entrez = x2y('ALIAS','ENTREZID')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname alias2ucsc
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
alias2ucsc = x2y('ALIAS','UCSCKG')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname alias2refseq
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
alias2refseq = x2y('ALIAS','REFSEQ')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname alias2ensembl
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
alias2ensembl = x2y('ALIAS','ENSEMBL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname symbol2entrez
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
symbol2entrez = x2y('SYMBOL','ENTREZID')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname symbol2ensembl
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
symbol2ensembl = x2y('SYMBOL','ENSEMBL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname symbol2refseq
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
symbol2refseq = x2y('SYMBOL','REFSEQ')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname symbol2ucsc
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
symbol2ucsc = x2y('SYMBOL','UCSCKG')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname symbol2alias
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
symbol2alias = x2y('SYMBOL','ALIAS')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname entrez2symbol
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
entrez2symbol = x2y('ENTREZID','SYMBOL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname entrez2ensembl
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
entrez2ensembl = x2y('ENTREZID','ENSEMBL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname entrez2refseq
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
entrez2refseq = x2y('ENTREZID','REFSEQ')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname entrez2ucsc
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
entrez2ucsc = x2y('ENTREZID','UCSCKG')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname entrez2alias
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
entrez2alias = x2y('ENTREZID','ALIAS')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname refseq2entrez
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
refseq2entrez = x2y('REFSEQ','ENTREZID')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname refseq2symbol
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
refseq2symbol = x2y('REFSEQ','SYMBOL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname refseq2ensembl
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
refseq2ensembl = x2y('REFSEQ','ENSEMBL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname refseq2ucsc
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
refseq2ucsc = x2y('REFSEQ','UCSCKG')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname refseq2alias
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
refseq2alias = x2y('REFSEQ','ALIAS')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname ucsc2symbol
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
ucsc2symbol = x2y('UCSCKG','SYMBOL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname ucsc2ensembl
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
ucsc2ensembl = x2y('UCSCKG','ENSEMBL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname ucsc2refseq
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
ucsc2refseq = x2y('UCSCKG','REFSEQ')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname ucsc2entrez
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
ucsc2entrez = x2y('UCSCKG','ENTREZ')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname ucsc2alias
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
ucsc2alias = x2y('UCSCKG','ALIAS')
jlaffy/scalop documentation built on March 24, 2024, 9 a.m.
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Defines functions x2y map_genes which_annotation is_annotation get_genes
Documented in get_genes is_annotation map_genes which_annotation x2y
### retrieve all genes/entries for a particular annotation type ###
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keytype PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname get_genes
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
get_genes = function(keytype) {
.genes = function() {
org = Homo.sapiens::Homo.sapiens
AnnotationDbi::keys(org, keytype=keytype)
}
}
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname get_ucsc
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
get_ucsc=get_genes('UCSCKG')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname get_refseq
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
get_refseq=get_genes('REFSEQ')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname get_symbols
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
get_symbols=get_genes('SYMBOL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname get_ensembl
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
get_ensembl=get_genes('ENSEMBL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname get_entrez
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
get_entrez=get_genes('ENTREZID')
### return annotation type ###
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keytype PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname is_annotation
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
is_annotation = function(keytype) {
.is_annotation = function(keys) {
org = Homo.sapiens::Homo.sapiens
universe = AnnotationDbi::keys(org, keytype=keytype)
keys %in% universe
}
}
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname is_symbol
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
is_symbol = is_annotation('SYMBOL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname is_entrez
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
is_entrez = is_annotation('ENTREZID')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname is_ensembl
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
is_ensembl = is_annotation('ENSEMBL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname is_refseq
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
is_refseq = is_annotation('REFSEQ')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname is_accnum
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
is_accnum = is_annotation('ACCNUM')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname is_alias
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
is_alias = is_annotation('ALIAS')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname is_ucsc
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys
is_ucsc = is_annotation('UCSCKG')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION
#' @param aliasesBeforeSymbols PARAM_DESCRIPTION, Default: FALSE
#' @param priority PARAM_DESCRIPTION, Default: NULL
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @rdname which_annotation
#' @export
which_annotation = function(keys, aliasesBeforeSymbols=FALSE, priority=NULL) {
keytypes = c('SYMBOL',
'ALIAS',
'ENTREZID',
'ENSEMBL',
'REFSEQ',
'ACCNUM',
'UCSCKG',
'TXID',
'ENSEMBLTRANS',
'ENSEMBLPROT',
'UNIPROT',
'UNIGENE',
'EXONID',
'ENZYME')
if (aliasesBeforeSymbols) {
if (!is.null(priority) && priority!='SYMBOL') keytypes[1:2] <- keytypes[2:1]
else message("You set priority to 'SYMBOL' so aliasesBeforeSymbols will be ignored.")
}
if (!is.null(priority)) {
if (!priority %in% keytypes) stop(priority, ' does not exist')
else keytypes = c(priority, setdiff(keytypes,priority))
}
.call = function(keytype) {
if (any(is.na(nams))) {nams[is.na(nams) & is_annotation(keytype)(keys)] <<- keytype}
}
nams = rep(NA,length(keys))
sapply(keytypes, .call)
setNames(nams, keys)
}
### map genes from one annotation type to others and return DF ###
### default return columns: SYMBOL, ENTREZID, TXCHROM ###
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keytype PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname map_genes
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys select
map_genes = function(keytype) {
.map_genes = function(keys=NULL, columns=NULL, add.columns=NULL, remove.columns=NULL) {
org = Homo.sapiens::Homo.sapiens
if (is.null(columns)) columns = c('SYMBOL','ENTREZID','TXCHROM')
columns = setdiff(columns,keytype)
columns = setdiff(columns,remove.columns)
columns = union(columns,add.columns)
if (is.null(keys)) {
keys = AnnotationDbi::keys(org, keytype=keytype)
}
AnnotationDbi::select(org,keys=keys,keytype=keytype,columns=columns)
}
}
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param columns PARAM_DESCRIPTION, Default: NULL
#' @param add.columns PARAM_DESCRIPTION, Default: NULL
#' @param remove.columns PARAM_DESCRIPTION, Default: NULL
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname map_entrez
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys select
map_entrez = map_genes('ENTREZID')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param columns PARAM_DESCRIPTION, Default: NULL
#' @param add.columns PARAM_DESCRIPTION, Default: NULL
#' @param remove.columns PARAM_DESCRIPTION, Default: NULL
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname map_symbol
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys select
map_symbol = map_genes('SYMBOL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param columns PARAM_DESCRIPTION, Default: NULL
#' @param add.columns PARAM_DESCRIPTION, Default: NULL
#' @param remove.columns PARAM_DESCRIPTION, Default: NULL
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname map_ensembl
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys select
map_ensembl = map_genes('ENSEMBL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param columns PARAM_DESCRIPTION, Default: NULL
#' @param add.columns PARAM_DESCRIPTION, Default: NULL
#' @param remove.columns PARAM_DESCRIPTION, Default: NULL
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname map_refseq
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys select
map_refseq = map_genes('REFSEQ')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param columns PARAM_DESCRIPTION, Default: NULL
#' @param add.columns PARAM_DESCRIPTION, Default: NULL
#' @param remove.columns PARAM_DESCRIPTION, Default: NULL
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname map_alias
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi keys select
map_alias = map_genes('ALIAS')
### convert between two keytypes ###
### this I think passes through ENTREZID ###
### if multiVals ='first', returns smallest ENTREZID
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param x PARAM_DESCRIPTION
#' @param y PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname x2y
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
x2y = function(x,y) {
.x2y = function(keys=NULL,multiVals='first') {
if (is.null(keys)) {
keys = get_genes(x)()
}
org = Homo.sapiens::Homo.sapiens
out=rep(NA,length(keys))
is.ready = is_annotation(y)(keys)
out[is.ready] <- keys[is.ready]
bool=!is.ready & is_annotation(x)(keys)
if (any(bool)) {
out[bool]<-AnnotationDbi::mapIds(org,
keys=keys[bool],
keytype=x,
column=y,
multiVals=multiVals)
}
out
}
}
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname alias2symbol
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
alias2symbol = x2y('ALIAS','SYMBOL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname alias2entrez
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
alias2entrez = x2y('ALIAS','ENTREZID')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname alias2ucsc
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
alias2ucsc = x2y('ALIAS','UCSCKG')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname alias2refseq
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
alias2refseq = x2y('ALIAS','REFSEQ')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname alias2ensembl
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
alias2ensembl = x2y('ALIAS','ENSEMBL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname symbol2entrez
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
symbol2entrez = x2y('SYMBOL','ENTREZID')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname symbol2ensembl
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
symbol2ensembl = x2y('SYMBOL','ENSEMBL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname symbol2refseq
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
symbol2refseq = x2y('SYMBOL','REFSEQ')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname symbol2ucsc
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
symbol2ucsc = x2y('SYMBOL','UCSCKG')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname symbol2alias
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
symbol2alias = x2y('SYMBOL','ALIAS')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname entrez2symbol
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
entrez2symbol = x2y('ENTREZID','SYMBOL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname entrez2ensembl
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
entrez2ensembl = x2y('ENTREZID','ENSEMBL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname entrez2refseq
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
entrez2refseq = x2y('ENTREZID','REFSEQ')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname entrez2ucsc
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
entrez2ucsc = x2y('ENTREZID','UCSCKG')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname entrez2alias
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
entrez2alias = x2y('ENTREZID','ALIAS')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname refseq2entrez
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
refseq2entrez = x2y('REFSEQ','ENTREZID')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname refseq2symbol
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
refseq2symbol = x2y('REFSEQ','SYMBOL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname refseq2ensembl
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
refseq2ensembl = x2y('REFSEQ','ENSEMBL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname refseq2ucsc
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
refseq2ucsc = x2y('REFSEQ','UCSCKG')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname refseq2alias
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
refseq2alias = x2y('REFSEQ','ALIAS')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname ucsc2symbol
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
ucsc2symbol = x2y('UCSCKG','SYMBOL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname ucsc2ensembl
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
ucsc2ensembl = x2y('UCSCKG','ENSEMBL')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname ucsc2refseq
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
ucsc2refseq = x2y('UCSCKG','REFSEQ')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname ucsc2entrez
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
ucsc2entrez = x2y('UCSCKG','ENTREZ')
#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param keys PARAM_DESCRIPTION, Default: NULL
#' @param multiVals PARAM_DESCRIPTION, Default: 'first'
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#' if(interactive()){
#' #EXAMPLE1
#' }
#' }
#' @seealso
#' \code{\link[Homo.sapiens]{Homo.sapiens}}
#' \code{\link[AnnotationDbi]{AnnotationDb-objects}}
#' @rdname ucsc2alias
#' @export
#' @importFrom Homo.sapiens Homo.sapiens
#' @importFrom AnnotationDbi mapIds
ucsc2alias = x2y('UCSCKG','ALIAS')
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