R/update_feature_annotations.R
In Selventa/RDataInfrastructure: What the package does (short line)
###################################################################################################=
## Similar to the "update_annotations.R" file, this file houses functions for
## updating platform feature annotation files (GPLs) from their default state
## (as downloaded from GEO).
###################################################################################################=
## The "Illumina human-6 v2.0 expression beadchip (extended)" chip.
UpdateFeatureAnnotations_GPL6370 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL6370 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
## Load biomaRt to be able to translate the nuIDs (Illumina's "nucleotide
## universal identifiers") into EGID.
# library(biomaRt)
# ensembl = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host="www.ensembl.org")
## Use Lumi to map the nuIDs to EGIDs
require(lumi)
require(lumiHumanIDMapping)
nuID.to.EGID.mapping <- nuID2EntrezID(nuID = NULL,
lib.mapping = 'lumiHumanIDMapping',
returnAllInfo = TRUE)
temp.idx <- match(annotations.df$NuID, rownames(nuID.to.EGID.mapping))
updated.columns <- cbind(nuID.to.EGID.mapping[temp.idx, c("EntrezID", "Symbol")],
Date=as.character(Sys.Date(), format="%b %d %Y"))
colnames(updated.columns) <- c("EGID", "GeneSymbol", "EGID_and_GeneSymbol_added_date")
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- cbind(annotations.df, updated.columns)
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL6370 platform annotation file to include EGIDs and Gene Symbols.\n")
} else {
cat("The GPL6370 platform annotation file didn't require updating.\n")
}
}
## The "Agilent Human 1A Oligo UNC custom Microarrays" chip.
UpdateFeatureAnnotations_GPL1390 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL1390 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
library(biomaRt)
ensembl <- useMart(biomart = 'ENSEMBL_MART_ENSEMBL', dataset="hsapiens_gene_ensembl", host="www.ensembl.org")
# tmp <- biomaRt::listAttributes(ensembl)
#
# possible.attributes <- grep("agilent", tmp$name, ignore.case=T, value=T)
#
#
# possible.attributes <- c(possible.attributes)
# annotations <- list()
# for (cur.attribute in possible.attributes) {
# annotations[[cur.attribute]] <- getBM(attributes=c(cur.attribute, "entrezgene"), mart=ensembl)
# print(cur.attribute)
# print(sum(annotations.df$SPOT_ID %in% annotations[[cur.attribute]][[cur.attribute]]))
#
# }
tmp.annotations <- getBM(attributes=c("efg_agilent_wholegenome_4x44k_v1", "entrezgene"), mart=ensembl)
egids.from.agilent <- tmp.annotations$entrezgene[match(annotations.df$SPOT_ID,
tmp.annotations$efg_agilent_wholegenome_4x44k_v1)]
sum(!is.na(egids.from.agilent))
tmp.annotations <- getBM(attributes=c("refseq_mrna", "entrezgene"), mart=ensembl)
egids.from.refseq <- tmp.annotations$entrezgene[match(annotations.df$Refseq.ID,
tmp.annotations$refseq_mrna)]
sum(!is.na(egids.from.refseq))
sum(!is.na(egids.from.refseq) | !is.na(egids.from.agilent))
#look for differences
diff.mapping <-
!is.na(egids.from.refseq) &
!is.na(egids.from.agilent) &
(egids.from.refseq != egids.from.agilent)
egids.from.refseq[diff.mapping] <- egids.from.agilent[diff.mapping] <- NA
annotations.df$EGID <- ifelse(is.na(egids.from.refseq),
egids.from.agilent,
egids.from.refseq)
annotations.df$EGID_added_date <- as.character(Sys.Date(), format="%b %d %Y")
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(annotations.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(annotations.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL1390 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL1390 platform annotation file didn't require updating.\n")
}
return(invisible(annotations.df))
}
##-----------------------------------------------------------------------------=
## GPL4133: "Agilent-014850 Whole Human Genome Microarray 4x44K G4112F" chip.
##------=
## The annotation file doesn't contain an explicitly-named "EGID" column, but
## does contain the EGIDs in it's "GENE" column, so simply add that column
## annotation if not already added.
##-----------------------------------------------------------------------------=
UpdateFeatureAnnotations_GPL4133 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL4133 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
## The EGID information is already contained in the "GENE" column.
updated.columns <- cbind(annotations.df$GENE,
Date=as.character(Sys.Date(), format="%b %d %Y"))
colnames(updated.columns) <- c("EGID", "EGID_added_date")
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- cbind(annotations.df, updated.columns)
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL4133 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL4133 platform annotation file didn't require updating.\n")
}
}
##-----------------------------------------------------------------------------=
## GPL7202: "Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F (Probe Name version)" chip.
##------=
## The annotation file doesn't contain an explicitly-named "EGID" column, but
## does contain the EGIDs in it's "GENE" column, so simply add that column
## annotation if not already added.
##-----------------------------------------------------------------------------=
UpdateFeatureAnnotations_GPL7202 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL7202 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
## The EGID information is already contained in the "GENE" column.
updated.columns <- cbind(annotations.df$GENE,
Date=as.character(Sys.Date(), format="%b %d %Y"))
colnames(updated.columns) <- c("EGID", "EGID_added_date")
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- cbind(annotations.df, updated.columns)
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL7202 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL7202 platform annotation file didn't require updating.\n")
}
}
##-----------------------------------------------------------------------------=
## GPL13497: "Agilent-026652 Whole Human Genome Microarray 4x44K v2 (Probe Name version)" chip.
##------=
## The annotation file doesn't contain an explicitly-named "EGID" column, but
## does contain the EGIDs in it's "GENE" column, so simply add that column
## annotation if not already added.
##-----------------------------------------------------------------------------=
UpdateFeatureAnnotations_GPL13497 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL13497 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
## The EGID information is already contained in the "GENE" column.
updated.columns <- cbind(annotations.df$GENE,
Date=as.character(Sys.Date(), format="%b %d %Y"))
colnames(updated.columns) <- c("EGID", "EGID_added_date")
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- cbind(annotations.df, updated.columns)
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL13497 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL13497 platform annotation file didn't require updating.\n")
}
}
##-----------------------------------------------------------------------------=
## GPL19943: "Agilent-027516 Human 180K Array (Probe name version)" chip.
##------=
## The annotation file doesn't contain an explicitly-named "EGID" column, but
## does contain the EGIDs in it's "GENE" column, so simply add that column
## annotation if not already added.
##-----------------------------------------------------------------------------=
UpdateFeatureAnnotations_GPL19943 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL19943 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
## The EGID information is already contained in the "geneID" column.
updated.columns <- cbind(annotations.df$geneID,
Date=as.character(Sys.Date(), format="%b %d %Y"))
colnames(updated.columns) <- c("EGID", "EGID_added_date")
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- cbind(annotations.df, updated.columns)
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL19943 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL19943 platform annotation file didn't require updating.\n")
}
}
##-----------------------------------------------------------------------------=
## GPL4134: "Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F (Feature Number version)" chip.
##------=
## The annotation file doesn't contain an explicitly-named "EGID" column, but
## does contain the EGIDs in it's "GENE" column, so simply add that column
## annotation if not already added.
##-----------------------------------------------------------------------------=
UpdateFeatureAnnotations_GPL4134 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL4134 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
## The EGID information is already contained in the "GENE" column.
updated.columns <- cbind(annotations.df$GENE,
Date=as.character(Sys.Date(), format="%b %d %Y"))
colnames(updated.columns) <- c("EGID", "EGID_added_date")
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- cbind(annotations.df, updated.columns)
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL4134 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL4134 platform annotation file didn't require updating.\n")
}
}
##-----------------------------------------------------------------------------=
## GPL10904: "Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F (Feature Number version)" chip.
##------=
## The annotation file doesn't contain an "EGID" column, but
## does contain the gene symbol in it's "ORF" column
##-----------------------------------------------------------------------------=
UpdateFeatureAnnotations_GPL10904 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL10904 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
gene.names <- annotations.df$ORF
library(org.Hs.eg.db)
EGIDs <- select(org.Hs.eg.db, keys=gene.names, columns = "ENTREZID", keytype="SYMBOL")
symbols.with.two.EGIDs <- EGIDs$SYMBOL[which(duplicated(EGIDs$SYMBOL))]
# things that map to two EGIDs should be mapped to neither (since we can't disambiguate)
EGIDs$ENTREZID[EGIDs$SYMBOL %in% symbols.with.two.EGIDs] <- NA
EGIDs <- unique(EGIDs)
stopifnot(setequal(EGIDs$SYMBOL, gene.names))
# now for those that didn't map as the true gene symbol, see if they offer a single
# match as a synonym
syn.EGIDs <- select(org.Hs.eg.db, keys=gene.names[is.na(EGIDs$ENTREZID)],
columns="ENTREZID",
keytype="ALIAS")
# get rid of entries that aren't aliases for any EGID
syn.EGIDs <- syn.EGIDs[!is.na(syn.EGIDs$ENTREZID),]
# get rid of entries for which we already have a mapping (ie, we have the true
# gene symbol for that EGID)
syn.EGIDs <- syn.EGIDs[!(syn.EGIDs$ENTREZID %in% EGIDs$ENTREZID),]
# get rid of gene names that are aliases for more than one EGID
genes.with.dup.EGIDs <- syn.EGIDs$ALIAS[duplicated(syn.EGIDs$ALIAS)]
syn.EGIDs <- syn.EGIDs[!(syn.EGIDs$ALIAS %in% genes.with.dup.EGIDs),]
# get rid of EGIDs that map to multiple aliases in the list
EGIDs.with.two.symbols <- syn.EGIDs$ENTREZID[which(duplicated(syn.EGIDs$ENTREZID))]
syn.EGIDs <- syn.EGIDs[!(syn.EGIDs$ENTREZID %in% EGIDs.with.two.symbols),]
# make sure we've got a 1-to-1 mapping
stopifnot(!any(duplicated(syn.EGIDs$ALIAS)))
stopifnot(!any(duplicated(syn.EGIDs$ENTREZID)))
# put the remaining EGIDs into the EGIDs object
EGIDs$ENTREZID[match(syn.EGIDs$ALIAS, EGIDs$SYMBOL)] <- syn.EGIDs$ENTREZID
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- data.frame(annotations.df,
EGID = as.numeric(EGIDs$ENTREZID[match(annotations.df$ORF, EGIDs$SYMBOL)]),
EGID_added_date = as.character(Sys.Date(), format="%b %d %Y"),
stringsAsFactors=F)
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL10904 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL10904 platform annotation file didn't require updating.\n")
}
}
##-----------------------------------------------------------------------------=
## GPL18943: " NimbleGen Human Gene Expression 12x135K Array [100718_HG18_opt_expr]" chip.
##------=
## The annotation file doesn't contain an explicitly-named "EGID" column, but
## does contain the EGIDs in it's "GENE" column, so simply add that column
## annotation if not already added.
##-----------------------------------------------------------------------------=
UpdateFeatureAnnotations_GPL18943 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL18943 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
## The EGID information is already contained in the "DESCRIPTION" column, but
## we need to strsplit to get it out.
desc.split <- strsplit(annotations.df$DESCRIPTION, ";")
gene.id.text <- lapply(desc.split,
function(cur.vec) {
grep("gene_id", cur.vec, value=T)
})
table(sapply(gene.id.text, length))
# ok, gene_id appears zero or one times per probe...
gene.id <- sapply(gene.id.text,
function(x) {
if (length(x)==0) {
return(NA_integer_)
} else {
stopifnot(length(x)==1)
cur.id <- sub(" gene_id ", "", x, fixed=T)
cur.id <- gsub("'", "", cur.id, fixed=T)
if (is.na(as.numeric(cur.id))) {
browser()
print(cur.id)
}
return(as.numeric(cur.id))
}
})
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- cbind(annotations.df,
data.frame(EGID=gene.id,
EGID_added_date=as.character(Sys.Date(), format="%b %d %Y")))
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL18943 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL18943 platform annotation file didn't require updating.\n")
}
}
##-----------------------------------------------------------------------------=
## GPL19462: " Illumina MouseRef-8 v2.0 expression beadchip (ILMN_SYMBOL)" chip.
##------=
## The annotation file doesn't contain an "EGID" column, but
## does contain the gene symbol in it's "ORF" column
##-----------------------------------------------------------------------------=
UpdateFeatureAnnotations_GPL19462 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL19462 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
gene.names <- annotations.df$ORF
library(org.Mm.eg.db)
EGIDs <- select(org.Mm.eg.db, keys=gene.names, columns = "ENTREZID", keytype="SYMBOL")
symbols.with.two.EGIDs <- EGIDs$SYMBOL[which(duplicated(EGIDs$SYMBOL))]
# things that map to two EGIDs should be mapped to neither (since we can't disambiguate)
EGIDs$ENTREZID[EGIDs$SYMBOL %in% symbols.with.two.EGIDs] <- NA
EGIDs <- unique(EGIDs)
stopifnot(setequal(EGIDs$SYMBOL, gene.names))
# now for those that didn't map as the true gene symbol, see if they offer a single
# match as a synonym
syn.EGIDs <- select(org.Mm.eg.db, keys=gene.names[is.na(EGIDs$ENTREZID)],
columns="ENTREZID",
keytype="ALIAS")
# get rid of entries that aren't aliases for any EGID
syn.EGIDs <- syn.EGIDs[!is.na(syn.EGIDs$ENTREZID),]
# get rid of entries for which we already have a mapping (ie, we have the true
# gene symbol for that EGID)
syn.EGIDs <- syn.EGIDs[!(syn.EGIDs$ENTREZID %in% EGIDs$ENTREZID),]
# get rid of gene names that are aliases for more than one EGID
genes.with.dup.EGIDs <- syn.EGIDs$ALIAS[duplicated(syn.EGIDs$ALIAS)]
syn.EGIDs <- syn.EGIDs[!(syn.EGIDs$ALIAS %in% genes.with.dup.EGIDs),]
# get rid of EGIDs that map to multiple aliases in the list
EGIDs.with.two.symbols <- syn.EGIDs$ENTREZID[which(duplicated(syn.EGIDs$ENTREZID))]
syn.EGIDs <- syn.EGIDs[!(syn.EGIDs$ENTREZID %in% EGIDs.with.two.symbols),]
# make sure we've got a 1-to-1 mapping
stopifnot(!any(duplicated(syn.EGIDs$ALIAS)))
stopifnot(!any(duplicated(syn.EGIDs$ENTREZID)))
# put the remaining EGIDs into the EGIDs object
EGIDs$ENTREZID[match(syn.EGIDs$ALIAS, EGIDs$SYMBOL)] <- syn.EGIDs$ENTREZID
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- data.frame(annotations.df,
EGID = as.numeric(EGIDs$ENTREZID[match(annotations.df$ORF, EGIDs$SYMBOL)]),
EGID_added_date = as.character(Sys.Date(), format="%b %d %Y"),
stringsAsFactors=F)
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL19462 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL19462 platform annotation file didn't require updating.\n")
}
}
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###################################################################################################=
## Similar to the "update_annotations.R" file, this file houses functions for
## updating platform feature annotation files (GPLs) from their default state
## (as downloaded from GEO).
###################################################################################################=
## The "Illumina human-6 v2.0 expression beadchip (extended)" chip.
UpdateFeatureAnnotations_GPL6370 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL6370 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
## Load biomaRt to be able to translate the nuIDs (Illumina's "nucleotide
## universal identifiers") into EGID.
# library(biomaRt)
# ensembl = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host="www.ensembl.org")
## Use Lumi to map the nuIDs to EGIDs
require(lumi)
require(lumiHumanIDMapping)
nuID.to.EGID.mapping <- nuID2EntrezID(nuID = NULL,
lib.mapping = 'lumiHumanIDMapping',
returnAllInfo = TRUE)
temp.idx <- match(annotations.df$NuID, rownames(nuID.to.EGID.mapping))
updated.columns <- cbind(nuID.to.EGID.mapping[temp.idx, c("EntrezID", "Symbol")],
Date=as.character(Sys.Date(), format="%b %d %Y"))
colnames(updated.columns) <- c("EGID", "GeneSymbol", "EGID_and_GeneSymbol_added_date")
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- cbind(annotations.df, updated.columns)
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL6370 platform annotation file to include EGIDs and Gene Symbols.\n")
} else {
cat("The GPL6370 platform annotation file didn't require updating.\n")
}
}
## The "Agilent Human 1A Oligo UNC custom Microarrays" chip.
UpdateFeatureAnnotations_GPL1390 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL1390 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
library(biomaRt)
ensembl <- useMart(biomart = 'ENSEMBL_MART_ENSEMBL', dataset="hsapiens_gene_ensembl", host="www.ensembl.org")
# tmp <- biomaRt::listAttributes(ensembl)
#
# possible.attributes <- grep("agilent", tmp$name, ignore.case=T, value=T)
#
#
# possible.attributes <- c(possible.attributes)
# annotations <- list()
# for (cur.attribute in possible.attributes) {
# annotations[[cur.attribute]] <- getBM(attributes=c(cur.attribute, "entrezgene"), mart=ensembl)
# print(cur.attribute)
# print(sum(annotations.df$SPOT_ID %in% annotations[[cur.attribute]][[cur.attribute]]))
#
# }
tmp.annotations <- getBM(attributes=c("efg_agilent_wholegenome_4x44k_v1", "entrezgene"), mart=ensembl)
egids.from.agilent <- tmp.annotations$entrezgene[match(annotations.df$SPOT_ID,
tmp.annotations$efg_agilent_wholegenome_4x44k_v1)]
sum(!is.na(egids.from.agilent))
tmp.annotations <- getBM(attributes=c("refseq_mrna", "entrezgene"), mart=ensembl)
egids.from.refseq <- tmp.annotations$entrezgene[match(annotations.df$Refseq.ID,
tmp.annotations$refseq_mrna)]
sum(!is.na(egids.from.refseq))
sum(!is.na(egids.from.refseq) | !is.na(egids.from.agilent))
#look for differences
diff.mapping <-
!is.na(egids.from.refseq) &
!is.na(egids.from.agilent) &
(egids.from.refseq != egids.from.agilent)
egids.from.refseq[diff.mapping] <- egids.from.agilent[diff.mapping] <- NA
annotations.df$EGID <- ifelse(is.na(egids.from.refseq),
egids.from.agilent,
egids.from.refseq)
annotations.df$EGID_added_date <- as.character(Sys.Date(), format="%b %d %Y")
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(annotations.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(annotations.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL1390 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL1390 platform annotation file didn't require updating.\n")
}
return(invisible(annotations.df))
}
##-----------------------------------------------------------------------------=
## GPL4133: "Agilent-014850 Whole Human Genome Microarray 4x44K G4112F" chip.
##------=
## The annotation file doesn't contain an explicitly-named "EGID" column, but
## does contain the EGIDs in it's "GENE" column, so simply add that column
## annotation if not already added.
##-----------------------------------------------------------------------------=
UpdateFeatureAnnotations_GPL4133 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL4133 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
## The EGID information is already contained in the "GENE" column.
updated.columns <- cbind(annotations.df$GENE,
Date=as.character(Sys.Date(), format="%b %d %Y"))
colnames(updated.columns) <- c("EGID", "EGID_added_date")
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- cbind(annotations.df, updated.columns)
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL4133 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL4133 platform annotation file didn't require updating.\n")
}
}
##-----------------------------------------------------------------------------=
## GPL7202: "Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F (Probe Name version)" chip.
##------=
## The annotation file doesn't contain an explicitly-named "EGID" column, but
## does contain the EGIDs in it's "GENE" column, so simply add that column
## annotation if not already added.
##-----------------------------------------------------------------------------=
UpdateFeatureAnnotations_GPL7202 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL7202 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
## The EGID information is already contained in the "GENE" column.
updated.columns <- cbind(annotations.df$GENE,
Date=as.character(Sys.Date(), format="%b %d %Y"))
colnames(updated.columns) <- c("EGID", "EGID_added_date")
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- cbind(annotations.df, updated.columns)
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL7202 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL7202 platform annotation file didn't require updating.\n")
}
}
##-----------------------------------------------------------------------------=
## GPL13497: "Agilent-026652 Whole Human Genome Microarray 4x44K v2 (Probe Name version)" chip.
##------=
## The annotation file doesn't contain an explicitly-named "EGID" column, but
## does contain the EGIDs in it's "GENE" column, so simply add that column
## annotation if not already added.
##-----------------------------------------------------------------------------=
UpdateFeatureAnnotations_GPL13497 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL13497 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
## The EGID information is already contained in the "GENE" column.
updated.columns <- cbind(annotations.df$GENE,
Date=as.character(Sys.Date(), format="%b %d %Y"))
colnames(updated.columns) <- c("EGID", "EGID_added_date")
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- cbind(annotations.df, updated.columns)
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL13497 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL13497 platform annotation file didn't require updating.\n")
}
}
##-----------------------------------------------------------------------------=
## GPL19943: "Agilent-027516 Human 180K Array (Probe name version)" chip.
##------=
## The annotation file doesn't contain an explicitly-named "EGID" column, but
## does contain the EGIDs in it's "GENE" column, so simply add that column
## annotation if not already added.
##-----------------------------------------------------------------------------=
UpdateFeatureAnnotations_GPL19943 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL19943 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
## The EGID information is already contained in the "geneID" column.
updated.columns <- cbind(annotations.df$geneID,
Date=as.character(Sys.Date(), format="%b %d %Y"))
colnames(updated.columns) <- c("EGID", "EGID_added_date")
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- cbind(annotations.df, updated.columns)
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL19943 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL19943 platform annotation file didn't require updating.\n")
}
}
##-----------------------------------------------------------------------------=
## GPL4134: "Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F (Feature Number version)" chip.
##------=
## The annotation file doesn't contain an explicitly-named "EGID" column, but
## does contain the EGIDs in it's "GENE" column, so simply add that column
## annotation if not already added.
##-----------------------------------------------------------------------------=
UpdateFeatureAnnotations_GPL4134 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL4134 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
## The EGID information is already contained in the "GENE" column.
updated.columns <- cbind(annotations.df$GENE,
Date=as.character(Sys.Date(), format="%b %d %Y"))
colnames(updated.columns) <- c("EGID", "EGID_added_date")
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- cbind(annotations.df, updated.columns)
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL4134 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL4134 platform annotation file didn't require updating.\n")
}
}
##-----------------------------------------------------------------------------=
## GPL10904: "Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F (Feature Number version)" chip.
##------=
## The annotation file doesn't contain an "EGID" column, but
## does contain the gene symbol in it's "ORF" column
##-----------------------------------------------------------------------------=
UpdateFeatureAnnotations_GPL10904 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL10904 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
gene.names <- annotations.df$ORF
library(org.Hs.eg.db)
EGIDs <- select(org.Hs.eg.db, keys=gene.names, columns = "ENTREZID", keytype="SYMBOL")
symbols.with.two.EGIDs <- EGIDs$SYMBOL[which(duplicated(EGIDs$SYMBOL))]
# things that map to two EGIDs should be mapped to neither (since we can't disambiguate)
EGIDs$ENTREZID[EGIDs$SYMBOL %in% symbols.with.two.EGIDs] <- NA
EGIDs <- unique(EGIDs)
stopifnot(setequal(EGIDs$SYMBOL, gene.names))
# now for those that didn't map as the true gene symbol, see if they offer a single
# match as a synonym
syn.EGIDs <- select(org.Hs.eg.db, keys=gene.names[is.na(EGIDs$ENTREZID)],
columns="ENTREZID",
keytype="ALIAS")
# get rid of entries that aren't aliases for any EGID
syn.EGIDs <- syn.EGIDs[!is.na(syn.EGIDs$ENTREZID),]
# get rid of entries for which we already have a mapping (ie, we have the true
# gene symbol for that EGID)
syn.EGIDs <- syn.EGIDs[!(syn.EGIDs$ENTREZID %in% EGIDs$ENTREZID),]
# get rid of gene names that are aliases for more than one EGID
genes.with.dup.EGIDs <- syn.EGIDs$ALIAS[duplicated(syn.EGIDs$ALIAS)]
syn.EGIDs <- syn.EGIDs[!(syn.EGIDs$ALIAS %in% genes.with.dup.EGIDs),]
# get rid of EGIDs that map to multiple aliases in the list
EGIDs.with.two.symbols <- syn.EGIDs$ENTREZID[which(duplicated(syn.EGIDs$ENTREZID))]
syn.EGIDs <- syn.EGIDs[!(syn.EGIDs$ENTREZID %in% EGIDs.with.two.symbols),]
# make sure we've got a 1-to-1 mapping
stopifnot(!any(duplicated(syn.EGIDs$ALIAS)))
stopifnot(!any(duplicated(syn.EGIDs$ENTREZID)))
# put the remaining EGIDs into the EGIDs object
EGIDs$ENTREZID[match(syn.EGIDs$ALIAS, EGIDs$SYMBOL)] <- syn.EGIDs$ENTREZID
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- data.frame(annotations.df,
EGID = as.numeric(EGIDs$ENTREZID[match(annotations.df$ORF, EGIDs$SYMBOL)]),
EGID_added_date = as.character(Sys.Date(), format="%b %d %Y"),
stringsAsFactors=F)
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL10904 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL10904 platform annotation file didn't require updating.\n")
}
}
##-----------------------------------------------------------------------------=
## GPL18943: " NimbleGen Human Gene Expression 12x135K Array [100718_HG18_opt_expr]" chip.
##------=
## The annotation file doesn't contain an explicitly-named "EGID" column, but
## does contain the EGIDs in it's "GENE" column, so simply add that column
## annotation if not already added.
##-----------------------------------------------------------------------------=
UpdateFeatureAnnotations_GPL18943 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL18943 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
## The EGID information is already contained in the "DESCRIPTION" column, but
## we need to strsplit to get it out.
desc.split <- strsplit(annotations.df$DESCRIPTION, ";")
gene.id.text <- lapply(desc.split,
function(cur.vec) {
grep("gene_id", cur.vec, value=T)
})
table(sapply(gene.id.text, length))
# ok, gene_id appears zero or one times per probe...
gene.id <- sapply(gene.id.text,
function(x) {
if (length(x)==0) {
return(NA_integer_)
} else {
stopifnot(length(x)==1)
cur.id <- sub(" gene_id ", "", x, fixed=T)
cur.id <- gsub("'", "", cur.id, fixed=T)
if (is.na(as.numeric(cur.id))) {
browser()
print(cur.id)
}
return(as.numeric(cur.id))
}
})
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- cbind(annotations.df,
data.frame(EGID=gene.id,
EGID_added_date=as.character(Sys.Date(), format="%b %d %Y")))
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL18943 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL18943 platform annotation file didn't require updating.\n")
}
}
##-----------------------------------------------------------------------------=
## GPL19462: " Illumina MouseRef-8 v2.0 expression beadchip (ILMN_SYMBOL)" chip.
##------=
## The annotation file doesn't contain an "EGID" column, but
## does contain the gene symbol in it's "ORF" column
##-----------------------------------------------------------------------------=
UpdateFeatureAnnotations_GPL19462 <- function( gpl.filename, gpl.path = getwd(), replace.original=TRUE ) {
## Read in the current GPL19462 platform annotation CSV file.
annotations.df <- read.csv(file = paste0(gpl.path, "/", gpl.filename), stringsAsFactors = FALSE)
## If there is no EGID (Entrez gene ID) column, then we will add one.
if (!("EGID" %in% colnames(annotations.df))) {
gene.names <- annotations.df$ORF
library(org.Mm.eg.db)
EGIDs <- select(org.Mm.eg.db, keys=gene.names, columns = "ENTREZID", keytype="SYMBOL")
symbols.with.two.EGIDs <- EGIDs$SYMBOL[which(duplicated(EGIDs$SYMBOL))]
# things that map to two EGIDs should be mapped to neither (since we can't disambiguate)
EGIDs$ENTREZID[EGIDs$SYMBOL %in% symbols.with.two.EGIDs] <- NA
EGIDs <- unique(EGIDs)
stopifnot(setequal(EGIDs$SYMBOL, gene.names))
# now for those that didn't map as the true gene symbol, see if they offer a single
# match as a synonym
syn.EGIDs <- select(org.Mm.eg.db, keys=gene.names[is.na(EGIDs$ENTREZID)],
columns="ENTREZID",
keytype="ALIAS")
# get rid of entries that aren't aliases for any EGID
syn.EGIDs <- syn.EGIDs[!is.na(syn.EGIDs$ENTREZID),]
# get rid of entries for which we already have a mapping (ie, we have the true
# gene symbol for that EGID)
syn.EGIDs <- syn.EGIDs[!(syn.EGIDs$ENTREZID %in% EGIDs$ENTREZID),]
# get rid of gene names that are aliases for more than one EGID
genes.with.dup.EGIDs <- syn.EGIDs$ALIAS[duplicated(syn.EGIDs$ALIAS)]
syn.EGIDs <- syn.EGIDs[!(syn.EGIDs$ALIAS %in% genes.with.dup.EGIDs),]
# get rid of EGIDs that map to multiple aliases in the list
EGIDs.with.two.symbols <- syn.EGIDs$ENTREZID[which(duplicated(syn.EGIDs$ENTREZID))]
syn.EGIDs <- syn.EGIDs[!(syn.EGIDs$ENTREZID %in% EGIDs.with.two.symbols),]
# make sure we've got a 1-to-1 mapping
stopifnot(!any(duplicated(syn.EGIDs$ALIAS)))
stopifnot(!any(duplicated(syn.EGIDs$ENTREZID)))
# put the remaining EGIDs into the EGIDs object
EGIDs$ENTREZID[match(syn.EGIDs$ALIAS, EGIDs$SYMBOL)] <- syn.EGIDs$ENTREZID
## Add the EGIDs and the current date onto the annotation data frame.
updated.annotation.df <- data.frame(annotations.df,
EGID = as.numeric(EGIDs$ENTREZID[match(annotations.df$ORF, EGIDs$SYMBOL)]),
EGID_added_date = as.character(Sys.Date(), format="%b %d %Y"),
stringsAsFactors=F)
## Write out the updated annotation data frame back to CSV (replacing
## the original annotation file if specified).
if (replace.original) {
write.csv(updated.annotation.df, file = paste0(gpl.path, "/", gpl.filename), row.names = FALSE)
} else {
write.csv(updated.annotation.df,
file = paste0(gpl.path, "/",
gsub(pattern = ".csv$",
replacement = "_updated.csv",
gpl.filename,
ignore.case = TRUE)),
row.names = FALSE)
}
cat("Updated the GPL19462 platform annotation file to include EGIDs.\n")
} else {
cat("The GPL19462 platform annotation file didn't require updating.\n")
}
}
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