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fix: add biomart mirror failover and improve ortholog mapping #425

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fix: add biomart mirror failover and improve ortholog mapping #425

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5c5fca2
fix: add biomart mirror failover and improve ortholog mapping
ivokwee Jan 16, 2026
e295b6f
correct if
ivokwee Jan 16, 2026
d144495
correct which
ivokwee Jan 16, 2026
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91 changes: 52 additions & 39 deletions R/pgx-annot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -125,7 +125,6 @@ getProbeAnnotation <- function(organism,
info("[getProbeAnnotation] annotating with custom annotation")
genes <- getCustomAnnotation2(probes0, annot_table)
} else if (datatype == "metabolomics") {
dbg("[getProbeAnnotation] annotating for metabolomics")
mx.check <- mx.check_mapping(
probes,
all.db = c("playdata", "annothub", "refmet"), check.first = TRUE
Expand All @@ -144,23 +143,19 @@ getProbeAnnotation <- function(organism,
dbg("[getProbeAnnotation] WARNING: not able to map metabolomics probes")
}
} else if (datatype == "lipidomics") {
dbg("[getProbeAnnotation] annotating for lipidomics")
## Directly annotate if probes are recognized
genes <- getLipidAnnotation(
probes,
extra_annot = TRUE,
annot_table = annot_table
)
} else if (datatype == "multi-omics") {
dbg("[getProbeAnnotation] annotating for multi-omics")
genes <- getMultiOmicsProbeAnnotation(organism, probes)
} else {
if (datatype == "proteomics") {
dbg("[getProbeAnnotation] annotating for proteomics")
is.phospho <- annotate_phospho_residue(probes, detect.only = TRUE)
genes <- getGeneAnnotation(organism = organism, probes = probes, is.phospho = is.phospho)
} else {
dbg("[getProbeAnnotation] annotating for transcriptomics")
genes <- getGeneAnnotation(organism = organism, probes = probes)
}
}
Expand Down Expand Up @@ -391,9 +386,6 @@ getGeneAnnotation.ANNOTHUB <- function(
cols <- unique(c(cols, "ENTREZID"))
}

dbg("[getGeneAnnotation.ANNOTHUB] annotation columns:", cols)
dbg("[getGeneAnnotation.ANNOTHUB] probe_type = ", probe_type)
dbg("[getGeneAnnotation.ANNOTHUB] retrieving annotation for ", length(probes), "features.")
suppressMessages(suppressWarnings(
annot <- AnnotationDbi::select(
orgdb,
Expand Down Expand Up @@ -465,17 +457,12 @@ getGeneAnnotation.ANNOTHUB <- function(
missing.probes <- missing.probes[!is.na(missing.probes)]
length(missing.probes)
if (second.pass && length(missing.probes)) {
dbg(
"[getGeneAnnotation.ANNOTHUB] second pass: retrying missing",
length(missing.probes), "symbols..."
)
missing.probe_type <- try(suppressWarnings(suppressMessages(
detect_probetype(organism, missing.probes, orgdb = orgdb)
)), silent = TRUE)
if (inherits(missing.probe_type, "try-error")) {
missing.probe_type <- NULL
}
dbg("[getGeneAnnotation.ANNOTHUB] missing.probe_type=", missing.probe_type)

## only do second try if missing.probetype is different

Expand Down Expand Up @@ -965,10 +952,6 @@ getCustomAnnotation2 <- function(probes, custom_annot, feature.col = "feature",
), 1)
if (length(ortholog.col) == 0) ortholog.col <- NA
}
dbg("[getCustomAnnotation2] feature.col = ", feature.col)
dbg("[getCustomAnnotation2] symbol.col = ", symbol.col)
dbg("[getCustomAnnotation2] title.col = ", gene_title.col)
dbg("[getCustomAnnotation2] ortholog.col = ", ortholog.col)

features <- custom_annot[, feature.col]
custom_annot <- custom_annot[match(probes, features), ]
Expand Down Expand Up @@ -1020,13 +1003,40 @@ getCustomAnnotation2 <- function(probes, custom_annot, feature.col = "feature",
## ================== GET ORTHOLOG FUNCTIONS ======================================
## ================================================================================

biomaRt.useEnsembl <- function(biomart, dataset=NULL,
mirrors = c("www","useast","asia")) {
mirror.ok <- rep(NA, length(mirrors))
names(mirror.ok) <- mirrors
m="www"
for(m in mirrors) {
resp <- NULL
resp <- biomaRt::useEnsembl(biomart = biomart, mirror = m)
mirror.ok[m] <- !(resp@host %in% c(NA,"",NULL))
}
mirror.ok
if(!any(mirror.ok)) {
message("WARNING: could not reach any biomart mirror")
return(NULL)
}
sel.mirror <- head(names(which(mirror.ok)),1)
sel.mirror
if(is.null(dataset)) {
mart <- biomaRt::useEnsembl(biomart = biomart, mirror = sel.mirror)
} else {
mart <- biomaRt::useEnsembl(biomart = biomart, dataset = dataset, mirror = sel.mirror)
}
return(mart)
}


#' @title Get human ortholog from given symbols of organism by using
#' orthogene package. This package needs internet connection.
#'
#' @export
getHumanOrtholog <- function(organism, symbols,
ortho.methods = c("homologene", "gprofiler", "babelgene"),
verbose = 1) {

orthogenes <- rep(NA, length(symbols))
orthosource <- rep(NA, length(symbols))

Expand Down Expand Up @@ -1096,8 +1106,7 @@ getHumanOrtholog <- function(organism, symbols,
nrow(ortho.out) > 0)
results.ok
if (results.ok) {
ii <- which(is.na(orthogenes))
## ii <- head(which(is.na(orthogenes)),10)
ii <- which(is.na(orthogenes)) ## still unmapped
jj <- match(symbols[ii], ortho.out$input_gene)
kk <- ii[which(!is.na(jj))]
jj <- jj[which(!is.na(jj))]
Expand All @@ -1110,26 +1119,24 @@ getHumanOrtholog <- function(organism, symbols,
ortho.found <- all(!is.na(orthogenes))
i <- i + 1
}

table(is.na(orthogenes))
mean.mapped <- round(100 * mean(!is.na(orthogenes)), digits = 4)
orthogene.failed <- (mean.mapped < 10.0)
orthogene.failed
if (orthogene.failed) {
if (verbose > 0) message("[getHumanOrtholog] ratio mapped using orthogene = ", mean.mapped, "%")
if (verbose > 0) message("[getHumanOrtholog] ratio mapped using orthogene = ", mean.mapped, "%")

if (any(is.na(orthogenes))) {
if (verbose > 0) message("[getHumanOrtholog] Trying biomart...")
## test if biomart is reachable
ii <- which(is.na(symbols))
ii <- which(is.na(orthogenes))
res.biomart <- try(getHumanOrtholog.biomart(organism, symbols[ii]), silent = TRUE)
class(res.biomart)
if (!"try-error" %in% class(res.biomart)) {
jj <- which(is.na(res.biomart))
ii <- ii[jj]
orthogenes[ii] <- res.biomart[jj]
orthosource[ii] <- "biomart"
} else {
if (verbose > 0) message("[getHumanOrtholog] biomart failed...")
}
} else {
if (verbose > 0) message("[getHumanOrtholog] skipping biomart...")
mean.mapped <- round(100 * mean(!is.na(orthogenes)), digits = 4)
message("[getHumanOrtholog] ratio mapped after biomart = ", mean.mapped, "%")
}

## Map any missing symbols that look like human genes
Expand Down Expand Up @@ -1166,7 +1173,13 @@ getHumanOrtholog.biomart <- function(organism, symbols, verbose = 1) {
organism0 <- paste0(s1, s2)
organism0
if (verbose > 0) message("[getHumanOrtholog.biomart] Searching biomart for '", organism0, "'")
dd <- listDatasets(useEnsembl(biomart = "genes"))

mart <- biomaRt.useEnsembl(biomart = "genes")
if(is.null(mart)) {
message("ERROR: no biomart mirrors reachable. Exiting.")
return(NULL)
}
dd <- listDatasets(mart)
hh <- grep(organism0, dd$dataset)
hh
if (length(hh) == 0) {
Expand All @@ -1178,8 +1191,8 @@ getHumanOrtholog.biomart <- function(organism, symbols, verbose = 1) {
if (verbose > 0) message("[getHumanOrtholog.biomart] found matching dataset '", dataset, "'")
organism_mart <- NULL
human_mart <- NULL
organism_mart <- biomaRt::useEnsembl(biomart = "genes", dataset = dataset)
human_mart <- biomaRt::useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")
organism_mart <- biomaRt.useEnsembl(biomart = "genes", dataset = dataset)
human_mart <- biomaRt.useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")
mart1.ok <- (!is.null(organism_mart) && !"try-error" %in% class(organism_mart) &&
class(organism_mart) == "Mart")
mart2.ok <- (!is.null(human_mart) && !"try-error" %in% class(human_mart) &&
Expand Down Expand Up @@ -1422,7 +1435,7 @@ detect_probetype <- function(organism, probes, orgdb = NULL,
if (tolower(organism) == "rat") organism <- "Rattus norvegicus"

if (is.null(datatype) && all(grepl("[:]", probes))) {
dbg("[detect_probetype] datatype is multi-omics")
dbg("[detect_probetype] datatype is multi-omics?")
datatype <- "multi-omics"
}

Expand Down Expand Up @@ -2454,8 +2467,7 @@ getMultiOmicsProbeAnnotation <- function(organism, probes) {
dtype <- ifelse(grepl("chebi|hmdb|kegg|pubchem|lipid|refmet", dtype), "mx", dtype)
table(dtype)
dtype[!dtype %in% c("gx","px","mx")] <- "custom"
table(dtype)
dbg("[getMultiOmicsProbeAnnotation] dtypes = ", unique(dtype))
dbg("[getMultiOmicsProbeAnnotation] detected datatypes = ", unique(dtype))

## populate with defaults
symbol <- sub("^[a-zA-Z]+:", "", probes)
Expand All @@ -2467,7 +2479,7 @@ getMultiOmicsProbeAnnotation <- function(organism, probes) {
aa <- getGeneAnnotation(organism, pp)
head(aa)
aa$data_type <- sub(":.*", "", probes[ii])
rownames(aa) <- probes[ii]
##rownames(aa) <- probes[ii]
aa$feature <- probes[ii]
annot[['gx']] <- aa
}
Expand All @@ -2478,7 +2490,7 @@ getMultiOmicsProbeAnnotation <- function(organism, probes) {
pp <- sub("^[a-zA-Z]+:", "", probes[ii])
aa <- getMetaboliteAnnotation(pp)
aa$data_type <- "mx"
rownames(aa) <- probes[ii]
##rownames(aa) <- probes[ii]
aa$feature <- probes[ii]
annot[['mx']] <- aa
}
Expand All @@ -2488,7 +2500,7 @@ getMultiOmicsProbeAnnotation <- function(organism, probes) {
aa <- getCustomAnnotation(pp, custom_annot = NULL)
head(aa)
aa$data_type <- "custom"
rownames(aa) <- probes[ii]
##rownames(aa) <- probes[ii]
aa$feature <- probes[ii]
annot[['custom']] <- aa
}
Expand All @@ -2507,8 +2519,9 @@ getMultiOmicsProbeAnnotation <- function(organism, probes) {
annot <- annot[match(probes, annot$feature), ]
rownames(annot) <- make_unique(probes)
head(annot)

## fill NA
annot$symbol[annot$symbol %in% c("-","")] <- NA
symbolx <- paste0("{",symbol,"}")
annot$human_ortholog[which(annot$human_ortholog == "")] <- NA
annot$feature <- ifelse(is.na(annot$feature), probes, annot$feature)
Expand Down
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