[BioC] Finding coding SNPs with predictCoding
Valerie Obenchain
vobencha at fhcrc.org
Sun Mar 4 05:23:35 CET 2012
Hi Thomas,
Thanks very much for the ideas and specific examples. These are very
helpful.
Take care,
Valerie
On 03/02/12 16:58, 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
>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioconductor mailing list
>>>>>> Bioconductor at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>> Search the archives:
>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor
mailing list