[BioC] Finding coding SNPs with predictCoding
Alex Gutteridge
alexg at ruggedtextile.com
Mon Mar 5 10:25:37 CET 2012
Hi Valerie,
I'd exactly echo what Thomas wrote (thanks Thomas!). My specific use
case is mapping coding SNPs to PDB protein structures, so something that
encodes 'His88 (CAT) -> Gln88 (CAA)' is all I need.
Alex Gutteridge.
On 03.03.2012 00:58, Thomas Girke wrote:
> Hi Valerie,
>
> Based on my experience the position in the complete protein (rather
> than
> CDS) sequence would be the most important piece of information to
> record
> here. For instance, if a SNP changes the 88th triplet CAT (His) in
> the
> ORF of a transcript to CAA (Gln) then you want to record it like
> this:
> His88 (CAT) -> Gln88 (CAA). This way the user can map this change to
> a
> protein structure or inject it into the corresponding protein
> sequence
> without any additional remapping or coding.
>
> Another feature to consider are SNPs affecting splice sites (commonly
> first and last two nucleotides of an intron).
>
> If possible it would be also very useful to support users who want to
> work with their custom genomes and annotations files provided as
> FASTA
> and GFF/GTF files, respectively.
>
> Best,
>
> Thomas
>
>
> On Fri, Mar 02, 2012 at 11:31:57PM +0000, Valerie Obenchain wrote:
>> Slight change to this -
>>
>> I'm now returning the following new columns,
>>
>> \item{\code{seqTxLoc}}{
>> Location in transcript-based coordinates of the first
>> nucleotide in
>> the codon sequence to be translated. This position
>> corresponds to the
>> first nucleotide in both the \code{refSeq} and \code{varSeq}
>> columns.
>> }
>> \item{\code{varTxLoc}}{
>> Location in transcript-based coordinates of the first
>> nucleotide in
>> the variant. This value will be the same as \code{seqTxLoc}
>> when the
>> variant starts exactly at the beginning of a codon.
>> }
>> \item{\code{varCdsLoc}}{
>> Location in cds-based coordinates of the first nucleotide in
>> the variant. This position is relative to the start of the
>> cds region
>> defined in the \code{subject} annotation.
>> }
>> \item{\code{subjStrand}}{
>> The strand of the \code{subject} the variant matched.
>> \code{predictCoding}
>> determines which variants fall in a coding region by finding
>> the
>> overlaps
>> between the \code{query} and \code{subject}. The \code{query}
>> may be
>> un-stranded \sQuote{*} but the \code{subject} annotation will
>> have a strand.
>> }
>>
>>
>> You are interested in 'protein coordinates'. Does 'varCdsLoc'
>> described
>> above meet the need or are you looking for the actual codon number
>> in
>> the coding sequence? I am interested in hearing more about what you
>> are
>> doing with the protein coordinates, how you are using them. It would
>> help us better design future functions.
>>
>> Thanks,
>> Valerie
>>
>> On 03/02/2012 01:11 AM, Alex Gutteridge wrote:
>> > Thanks Valerie - much appreciated!
>> >
>> > On 01.03.2012 21:30, Valerie Obenchain wrote:
>> >> A 'txLoc' column has been added to the output of predictCoding.
>> >> Available in devel version 1.1.57.
>> >>
>> >> Valerie
>> >>
>> >>
>> >> On 02/28/2012 08:20 AM, Valerie Obenchain wrote:
>> >>> Good suggestion. Yes, predictCoding is does this internally.
>> I'll
>> >>> post back here when this has been added.
>> >>>
>> >>> Valerie
>> >>>
>> >>>
>> >>>
>> >>> On 02/28/2012 01:49 AM, Alex Gutteridge wrote:
>> >>>> Hi Valerie,
>> >>>>
>> >>>> Thanks everything works great now. One small feature request -
>> >>>> would it be hard to output the protein sequence position of the
>> >>>> coding SNPs? At the moment once I've run predictCoding I'm
>> >>>> re-extracting the cds and working out the position of each
>> coding
>> >>>> SNP so I can see where in the protein sequence it is, but it
>> seems
>> >>>> like this is probably just replicating what predictCoding must
>> be
>> >>>> doing internally anyway?
>> >>>>
>> >>>> Alex Gutteridge
>> >>>
>> >>>
>> >>> On 02/24/2012 10:39 AM, Valerie Obenchain wrote:
>> >>>> Hi Alex,
>> >>>>
>> >>>> Thanks for the bug report. The cdsID was taken from an overlap
>> >>>> between the query and GRangesList of cds by transcripts. This
>> gave
>> >>>> the correct transcript number but (incorrectly) took the first
>> cds
>> >>>> number in the list by default. Now fixed in devel 1.1.55.
>> >>>>
>> >>>> I've also updated the man page.
>> >>>>
>> >>>> Valerie
>> >>>>
>> >>>>
>> >>>>
>> >>>> On 02/24/2012 02:08 AM, Alex Gutteridge wrote:
>> >>>>> On 22.02.2012 18:58, Herv? Pag?s wrote:
>> >>>>>> Hi Alex,
>> >>>>>>
>> >>>>>> On 02/22/2012 03:56 AM, Alex Gutteridge wrote:
>> >>>>>
>> >>>>> [...]
>> >>>>>
>> >>>>>>> But the predictCoding call gives this error:
>> >>>>>>>
>> >>>>>>> Error in .setSeqNames(x, value) :
>> >>>>>>> The replacement value for isActiveSeq must be a logical
>> vector,
>> >>>>>>> with
>> >>>>>>> names that match the seqlevels of the object
>> >>>>>>
>> >>>>>> The error message doesn't help much but I think the pb is
>> that you
>> >>>>>> didn't rename chMT properly. Try to do this:
>> >>>>>>
>> >>>>>> seqlevels(snps) <- gsub("chrMT", "chrM", seqlevels(snps))
>> >>>>>>
>> >>>>>> before you start the for(eg in entrez.ids){..} loop again.
>> >>>>>>
>> >>>>>> Cheers,
>> >>>>>> H.
>> >>>>>
>> >>>>> Thanks Herv? that nailed it. I'm having some difficulty
>> joining up
>> >>>>> the output of predictCoding() with the query SNPs though. If
>> >>>>> someone could point out where the disconnect in my thinking is
>> I
>> >>>>> would appreciate it!
>> >>>>>
>> >>>>> Here's my (now edited down) script:
>> >>>>>
>> >>>>> library(BSgenome.Hsapiens.UCSC.hg19)
>> >>>>> library(VariantAnnotation)
>> >>>>> library(SNPlocs.Hsapiens.dbSNP.20110815)
>> >>>>> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
>> >>>>>
>> >>>>> entrez.ids = c('6335')
>> >>>>> txdb19 = TxDb.Hsapiens.UCSC.hg19.knownGene
>> >>>>>
>> >>>>> snps = getSNPlocs(c("ch1","ch2"),as.GRanges=T)
>> >>>>> seqlevels(snps) <- gsub("ch", "chr", seqlevels(snps))
>> >>>>> seqlevels(snps) <- gsub("chrMT", "chrM", seqlevels(snps))
>> >>>>>
>> >>>>> gene.list = cdsBy(txdb19, by="gene")
>> >>>>> vsd.list = gene.list[entrez.ids]
>> >>>>> cds.list = cdsBy(txdb19,by="tx")
>> >>>>>
>> >>>>> eg = entrez.ids[1]
>> >>>>>
>> >>>>> snp.idx = unique(queryHits(findOverlaps(snps,
>> vsd.list[[eg]])))
>> >>>>> eg.snps = snps[snp.idx]
>> >>>>> iupac = values(eg.snps)[,"alleles_as_ambig"]
>> >>>>> eg.snps.exp = rep(eg.snps, nchar(IUPAC_CODE_MAP[iupac]))
>> >>>>> variant.alleles =
>> >>>>>
>> DNAStringSet(strsplit(paste(IUPAC_CODE_MAP[iupac],collapse=""),"")[[1]])
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> aa =
>> >>>>>
>> predictCoding(eg.snps.exp,txdb19,seqSource=Hsapiens,varAllele=variant.alleles)
>> >>>>>
>> >>>>> #####
>> >>>>>
>> >>>>> Then if I query the predictCoding results in aa in an
>> interactive
>> >>>>> session I get the following (see inline comments for what I
>> think
>> >>>>> should be happening, but I must be misinterpreting what
>> queryID
>> >>>>> means)
>> >>>>>
>> >>>>> The docs for predictCoding() contain a small typo
>> >>>>> (s/queryHits/queryID), but otherwise seem clear?
>> >>>>>
>> >>>>> Columns include ?queryID?, ?consequence?, ?refSeq?, ?varSeq?,
>> >>>>> ?refAA?, ?varAA?, ?txID?, ?geneID?, and ?cdsID?.
>> >>>>>
>> >>>>> ?queryHits? The ?queryHits? column provides a map back to
>> the
>> >>>>> variants in the original ?query?. If the ?query? was
>> a
>> >>>>> ?VCF?
>> >>>>> object this index corresponds to the row in the
>> >>>>> ?GRanges? in
>> >>>>> the ?rowData? slot. If ?query? was an expanded
>> ?GRanges?,
>> >>>>> ?RangedData? or ?RangesList? the index corresponds
>> to
>> >>>>> the row
>> >>>>> in the expanded object.
>> >>>>>
>> >>>>> #####
>> >>>>>
>> >>>>>> aa[1,]
>> >>>>> DataFrame with 1 row and 9 columns
>> >>>>> queryID consequence refSeq varSeq
>> refAA
>> >>>>> <integer> <factor> <DNAStringSet> <DNAStringSet> <AAStringSet>
>> >>>>> 1 1 nonsynonymous CTC ATC
>> L
>> >>>>> varAA txID geneID cdsID
>> >>>>> <AAStringSet> <character> <factor> <integer>
>> >>>>> 1 I 10921 6335 33668
>> >>>>>> #So the first SNP (queryID: 1) is nonsynonymous and maps to
>> tx
>> >>>>>> '10921' and cds '33668'.
>> >>>>>> #If I look at the first query SNP I get this:
>> >>>>>> eg.snps.exp[aa[1,'queryID'],]
>> >>>>> GRanges with 1 range and 2 elementMetadata values:
>> >>>>> seqnames ranges strand | RefSNP_id
>> >>>>> alleles_as_ambig
>> >>>>> <Rle> <IRanges> <Rle> | <character> <character>
>> >>>>> [1] chr2 [167055370, 167055370] * | 111558968
>> >>>>> R
>> >>>>> ---
>> >>>>> seqlengths:
>> >>>>> chr1 chr2 chr3 chr4 chr5 chr6 ... chr20 chr21 chr22
>> chrX
>> >>>>> chrY chrM
>> >>>>> NA NA NA NA NA NA ... NA NA NA
>> NA
>> >>>>> NA NA
>> >>>>>> #So SNP 1 is at 167055370 on chr2
>> >>>>>> #But if I check tx '10921' I see that the cds overlapping
>> >>>>>> 167055370 is actually '33651'
>> >>>>>> #And cds '33668' is at the other end of the tx:
>> >>>>>> cds.list[[aa[1,'txID']]]
>> >>>>> GRanges with 26 ranges and 3 elementMetadata values:
>> >>>>> seqnames ranges strand | cds_id
>> >>>>> cds_name
>> >>>>> <Rle> <IRanges> <Rle> | <integer> <character>
>> >>>>> [1] chr2 [167168009, 167168266] - | 33668
>> <NA>
>> >>>>> [2] chr2 [167163466, 167163584] - | 33667
>> <NA>
>> >>>>> [3] chr2 [167163020, 167163109] - | 33666
>> <NA>
>> >>>>> [4] chr2 [167162302, 167162430] - | 33647
>> <NA>
>> >>>>> [5] chr2 [167160748, 167160839] - | 33646
>> <NA>
>> >>>>> [6] chr2 [167159600, 167159812] - | 33645
>> <NA>
>> >>>>> [7] chr2 [167151109, 167151172] - | 33644
>> <NA>
>> >>>>> [8] chr2 [167149741, 167149882] - | 33643
>> <NA>
>> >>>>> [9] chr2 [167144947, 167145153] - | 33642
>> <NA>
>> >>>>> ... ... ... ... ... ...
>> >>>>> ...
>> >>>>> [18] chr2 [167099012, 167099166] - | 33659
>> <NA>
>> >>>>> [19] chr2 [167094604, 167094777] - | 33658
>> <NA>
>> >>>>> [20] chr2 [167089850, 167089972] - | 33657
>> <NA>
>> >>>>> [21] chr2 [167085201, 167085482] - | 33656
>> <NA>
>> >>>>> [22] chr2 [167084180, 167084233] - | 33655
>> <NA>
>> >>>>> [23] chr2 [167083077, 167083214] - | 33654
>> <NA>
>> >>>>> [24] chr2 [167060870, 167060974] - | 33653
>> <NA>
>> >>>>> [25] chr2 [167060465, 167060735] - | 33652
>> <NA>
>> >>>>> [26] chr2 [167055182, 167056374] - | 33651
>> <NA>
>> >>>>> exon_rank
>> >>>>> <integer>
>> >>>>> [1] 2
>> >>>>> [2] 3
>> >>>>> [3] 4
>> >>>>> [4] 5
>> >>>>> [5] 6
>> >>>>> [6] 7
>> >>>>> [7] 8
>> >>>>> [8] 9
>> >>>>> [9] 10
>> >>>>> ... ...
>> >>>>> [18] 19
>> >>>>> [19] 20
>> >>>>> [20] 21
>> >>>>> [21] 22
>> >>>>> [22] 23
>> >>>>> [23] 24
>> >>>>> [24] 25
>> >>>>> [25] 26
>> >>>>> [26] 27
>> >>>>> ---
>> >>>>> seqlengths:
>> >>>>> chr1 chr2 ...
>> >>>>> chr18_gl000207_random
>> >>>>> 249250621 243199373 ...
>> >>>>> 4262
>> >>>>>
>> >>>>>
>> >>>>
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--
Alex Gutteridge
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