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####============================================================
## Methods and functions to allow usage of EnsDb objects also
## with genomic resources that do not use Ensembl based
## seqnames
## We're storing the seqname style into the .properties slot
## of the EnsDb object.
####------------------------------------------------------------
.ENSOPT.SEQNOTFOUND="ensembldb.seqnameNotFound"
####============================================================
## formatSeqnamesForQuery
##
## Formating/renamaing the seqname(s) according to the specified
## style.
## x is an EnsDb,
## sn the seqnames to convert...
## If a seqname can not be mapped NA will be returned.
####------------------------------------------------------------
setMethod("formatSeqnamesForQuery", "EnsDb", function(x, sn, ifNotFound){
return(.formatSeqnameByStyleForQuery(x, sn, ifNotFound))
})
## Little helper function that returns eventually the argument.
## Returns MISSING if the argument was not set.
.getSeqnameNotFoundOption <- function(){
notFound <- "MISSING"
if(any(names(options()) == .ENSOPT.SEQNOTFOUND)){
notFound <- getOption(.ENSOPT.SEQNOTFOUND)
## Do some sanity checks?
}
return(notFound)
}
.formatSeqnameByStyleForQuery <- function(x, sn, ifNotFound){
## Fixing ifNotFound, allowing that this can be set using options.
if(missing(ifNotFound)){
ifNotFound <- .getSeqnameNotFoundOption()
}
## Map whatever to Ensembl seqnames, such that we can perform queries.
## Use mapSeqlevels, or rather genomeStyles and do it hand-crafted!
sst <- seqlevelsStyle(x)
dbSst <- dbSeqlevelsStyle(x)
if(sst == dbSst)
return(sn)
map <- getProperty(x, "genomeStyle")
if(!is(map, "data.frame"))
map <- genomeStyles(organism(x))
## sn are supposed to be in sst style, map them to dbSst
idx <- match(sn, map[, sst])
mapped <- map[idx, dbSst]
if(any(is.na(mapped))){
noMap <- which(is.na(mapped))
seqNoMap <- unique(sn[noMap])
if(length(seqNoMap) > 5){
theMess <- paste0("More than 5 seqnames could not be mapped to ",
"the seqlevels style of the database (", dbSst, ")!")
}else{
theMess <- paste0("Seqnames: ", paste(seqNoMap, collapse=", "),
" could not be mapped to ",
" the seqlevels style of the database (", dbSst, ")!")
}
if(is.na(ifNotFound) | is.null(ifNotFound)){
## Replacing the missing seqname mappings with ifNotFound.
mapped[noMap] <- ifNotFound
warnMess <- paste0(" Returning ", ifNotFound, " for these.")
}else{
## If MISSING -> STOP
if(ifNotFound == "MISSING"){
stop(theMess)
}else{
## Next special case: use the original names, i.e. don't map at all.
if(ifNotFound == "ORIGINAL"){
mapped[noMap] <- sn[noMap]
warnMess <- "Returning the orginal seqnames for these."
}else{
mapped[noMap] <- ifNotFound
warnMess <- paste0(" Returning ", ifNotFound, " for these.")
}
}
}
warning(theMess, warnMess)
}
return(mapped)
}
setMethod("formatSeqnamesFromQuery", "EnsDb", function(x, sn, ifNotFound){
return(.formatSeqnameByStyleFromQuery(x, sn, ifNotFound))
})
.formatSeqnameByStyleFromQuery <- function(x, sn, ifNotFound){
## Fixing ifNotFound, allowing that this can be set using options.
if(missing(ifNotFound)){
ifNotFound <- .getSeqnameNotFoundOption()
}
## Map Ensembl seqnames resulting form queries to the seqlevel style by
## seqlevelsStyle.
sst <- seqlevelsStyle(x)
dbSst <- dbSeqlevelsStyle(x)
if(sst == dbSst)
return(sn)
## Otherwise...
map <- getProperty(x, "genomeStyle")
if(!is(map, "data.frame"))
map <- genomeStyles(organism(x))
## sn are supposed to be in sst style, map them to dbSst
idx <- match(sn, map[, dbSst])
mapped <- map[idx, sst]
if(any(is.na(mapped))){
noMap <- which(is.na(mapped))
seqNoMap <- unique(sn[noMap])
if(length(seqNoMap) > 5){
theMess <- paste0("More than 5 seqnames with seqlevels style of the database (",
dbSst, ") could not be mapped to the seqlevels style: ",
sst, "!)")
}else{
theMess <- paste0("Seqnames: ", paste(seqNoMap, collapse=", "),
" with seqlevels style of the database (", dbSst,
") could not be mapped to seqlevels style: ", sst,
"!")
}
if(is.na(ifNotFound) | is.null(ifNotFound)){
## Replacing the missing seqname mappings with ifNotFound.
mapped[noMap] <- ifNotFound
warnMess <- paste0(" Returning ", ifNotFound, " for these.")
}else{
## If MISSING -> STOP
if(ifNotFound == "MISSING"){
stop(theMess)
}else{
## Next special case: use the original names, i.e. don't map at all.
if(ifNotFound == "ORIGINAL"){
mapped[noMap] <- sn[noMap]
warnMess <- " Returning the orginal seqnames for these."
}else{
mapped[noMap] <- ifNotFound
warnMess <- paste0(" Returning ", ifNotFound, " for these.")
}
}
}
warning(theMess, warnMess)
}
return(mapped)
}
####============================================================
## dbSeqlevelsStyle
##
## Returns the seqname style used by the database. Defaults to
## Ensembl and reads the property: dbSeqlevelsStyle.
####------------------------------------------------------------
setMethod("dbSeqlevelsStyle", "EnsDb", function(x){
stl <- getProperty(x, "dbSeqlevelsStyle")
if(is.na(stl))
stl <- "Ensembl"
return(stl)
})
####============================================================
## seqlevelStyle
##
## Get or set the seqlevel style. If we can't find the stype in
## GenomeInfoDb throw and error.
####------------------------------------------------------------
setMethod("seqlevelsStyle", "EnsDb", function(x){
st <- getProperty(x, "seqlevelsStyle")
if(is.na(st))
st <- "Ensembl"
return(st)
})
setReplaceMethod("seqlevelsStyle", "EnsDb", function(x, value){
if(value == dbSeqlevelsStyle(x)){
## Not much to do; that's absolutely fine.
x <- setProperty(x, seqlevelsStyle=value)
}else{
## Have to check whether I have the mapping available in GenomeInfoDb, if not
## -> throw an error.
dbStyle <- dbSeqlevelsStyle(x)
## Note that both, the db seqlevel style and the style have to be available!
## Check if we could use the mapping provided by GenomeInfoDb.
genSt <- try(genomeStyles(organism(x)), silent=TRUE)
if(is(genSt, "try-error")){
stop("No mapping of seqlevel styles available in GenomeInfoDb for",
" species ", organism(x), "! Please refer to the Vignette of the",
" GenomeInfoDb package if you would like to provide this mapping.")
}
if(!any(colnames(genSt) == value)){
stop("The provided seqlevels style is not known to GenomeInfoDb!")
}
if(!any(colnames(genSt) == dbStyle)){
stop("The seqlevels style of the database (", dbStyle,
") is not known to GenomeInfoDb!")
}
## If we got that far it should be OK
x <- setProperty(x, seqlevelsStyle=value)
x <- setProperty(x, genomeStyle=list(genSt))
}
return(x)
})
####============================================================
## supportedSeqlevelsStyles
##
## Get all supported seqlevels styles for the species of the EnsDb
####------------------------------------------------------------
setMethod("supportedSeqlevelsStyles", "EnsDb", function(x){
map <- genomeStyles(organism(x))
cn <- colnames(map)
cn <- cn[!(cn %in% c("circular", "auto", "sex"))]
return(colnames(cn))
})
####==================== OLD STUFF BELOW ====================
###==============================================================
## Prefix chromosome names with "chr" if ucscChromosomeNames option
## is set, otherwise, use chromosome names "as is".
## This function should be used in functions that return results from
## EnsDbs.
###--------------------------------------------------------------
prefixChromName <- function(x, prefix="chr"){
ucsc <- getOption("ucscChromosomeNames", default=FALSE)
if(ucsc){
## TODO fix also the mitochondrial chromosome name.
mapping <- ucscToEnsMapping()
for(i in 1:length(mapping)){
x <- sub(x, pattern=names(mapping)[i], replacement=mapping[i],
fixed=TRUE)
}
## Replace chr if it's already there
x <- gsub(x, pattern="^chr", replacement="", ignore.case=TRUE)
x <- paste0(prefix, x)
}
return(x)
}
###==============================================================
## Remove leading "chr" to fit Ensembl based chromosome names.
## This function should be called in functions that fetch data from
## EnsDbs.
###--------------------------------------------------------------
ucscToEns <- function(x){
## TODO rename all additional chromosome names.
mapping <- ucscToEnsMapping()
for(i in 1:length(mapping)){
x <- sub(x, pattern=mapping[i], replacement=names(mapping)[i],
fixed=TRUE)
}
x <- gsub(x, pattern="^chr", replacement="", ignore.case=TRUE)
return(x)
}
###============================================================
## Returns a character vector, elements representing UCSC chromosome
## names with their names corresponding to the respective Ensembl
## chromosome names.
###------------------------------------------------------------
ucscToEnsMapping <- function(){
theMap <- c(MT="chrM")
return(theMap)
}
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