[Bioc-devel] mapping vector of gene ids to gene symbols

Let's say I have a vector of gene IDs where some are NA, and are some are
repeated, and I want to map them to gene symbols, where I get NAs for the
NA IDs or IDs without a symbol. What is the best way to do this?

I tried select() but it gave me a table with unique entries; not very
convenient. It also does not handle NAs. And totally breaks with duplicates
using the GENEID key type (kind of works with ENTREZID):

select(Homo.sapiens, GENEID, "SYMBOL", "GENEID")
Error in `[[<-`(`*tmp*`, name, value = list(GENEID = c("245938", "245939",
:
   269 elements in value to replace 1312 elements

Also tried the venerable mget(GENEID, org.Hs.egSYMBOL, ifnotfound=NA), but
this returns a list and fails with NAs.

What would be nice is something like:

map(Homo.sapiens, GENEID, "SYMBOL", "GENEID", OneToOneOrNone)

where OneToOneOrNone is an assertion that I expect the mappings to be
one-to-one, so it will unlist() or whatever and throw an error if the
assertion fails. It should return NA for anything not found, and for any NA
GENEID. Does something like this already exist?

Michael

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Wow, VariantFiltering is awesome. It's impressive how it integrates all
of the annotation resources so seamlessly. And the shiny app looks very
useful. This should be a model package for where we want to bring
Bioconductor.

You should look into using VRanges instead of GRanges for the return
value of filteredVariants(). It can record the provenance of the filters
if you are using the FilterRules framework. And ReportingTools may be
useful for generating semi-interactive HTML reports.

I'm going to use this in the course next week at Brixen. My tutorial is
already based on the CEU trio, so the vignette integrates perfectly.

Nice work,
Michael


On Wed, Jun 18, 2014 at 6:20 AM, Robert Castelo <robert.castelo at upf.edu
<mailto:robert.castelo at upf.edu>> wrote:

    hi Michael,

    this souns like if you had a list of variants where you have
    annotated their Entrez Gene IDs, which sometimes are NA because
    those variance do not overlap any gene and sometimes are repeated
    Entrez Gene IDs when two or more of those variants overlap the same
    gene :)

    at least is the situation i had when programming the
    VariantFiltering package, i also could not find a one-liner solution
    but you might want to look to what i ended up doing there, in case
    it might be also useful for you.

    you'll find it in the method "annotateVariants" that dispatches
    "OrgDb" objects (i.e., gene-centric annotation packages), within
    VariantFiltering/R/__annotationEngine.R

    if you take a look at it, do not hesitate to comment if you have any
    suggestion to improve this. i also look forward to the
    annotation-gurus feedback on this question :)

    cheers,

    robert.


    On 06/18/2014 03:03 PM, Michael Lawrence wrote:

        Let's say I have a vector of gene IDs where some are NA, and are
        some are
        repeated, and I want to map them to gene symbols, where I get
        NAs for the
        NA IDs or IDs without a symbol. What is the best way to do this?

        I tried select() but it gave me a table with unique entries; not
        very
        convenient. It also does not handle NAs. And totally breaks with
        duplicates
        using the GENEID key type (kind of works with ENTREZID):

        select(Homo.sapiens, GENEID, "SYMBOL", "GENEID")
        Error in `[[<-`(`*tmp*`, name, value = list(GENEID = c("245938",
        "245939",
        :
            269 elements in value to replace 1312 elements

        Also tried the venerable mget(GENEID, org.Hs.egSYMBOL,
        ifnotfound=NA), but
        this returns a list and fails with NAs.

        What would be nice is something like:

        map(Homo.sapiens, GENEID, "SYMBOL", "GENEID", OneToOneOrNone)

        where OneToOneOrNone is an assertion that I expect the mappings
        to be
        one-to-one, so it will unlist() or whatever and throw an error
        if the
        assertion fails. It should return NA for anything not found, and
        for any NA
        GENEID. Does something like this already exist?

        Michael

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Let's say I have a vector of gene IDs where some are NA, and are some are
repeated, and I want to map them to gene symbols, where I get NAs for the
NA IDs or IDs without a symbol. What is the best way to do this?

I tried select() but it gave me a table with unique entries; not very
convenient. It also does not handle NAs. And totally breaks with duplicates
using the GENEID key type (kind of works with ENTREZID):

select(Homo.sapiens, GENEID, "SYMBOL", "GENEID")
Error in `[[<-`(`*tmp*`, name, value = list(GENEID = c("245938", "245939",
:
   269 elements in value to replace 1312 elements

Also tried the venerable mget(GENEID, org.Hs.egSYMBOL, ifnotfound=NA), but
this returns a list and fails with NAs.

What would be nice is something like:

map(Homo.sapiens, GENEID, "SYMBOL", "GENEID", OneToOneOrNone)

where OneToOneOrNone is an assertion that I expect the mappings to be
one-to-one, so it will unlist() or whatever and throw an error if the
assertion fails. It should return NA for anything not found, and for any NA
GENEID. Does something like this already exist?

Michael

	[[alternative HTML version deleted]]