[BioC] GWATools use in creating ncdf files
Stephanie M. Gogarten
sdmorris at u.washington.edu
Wed Jun 5 18:11:40 CEST 2013
It's not finding any BAF values that meet all the criteria (snpID in
"snp.ids", chromosome in "chrom.ids", genotype is heterozygous or
missing, BAF is non-missing).
Is it possible for you to send me the data you're using, along with your
values of "scan.ids", "chrom.ids", and "snp.ids"?
Stephanie
On 6/4/13 2:23 PM, Sam Rose wrote:
> Yes this was intentional. I just wanted to get it running for one sample
> and then expand to the rest. I was also limiting this to only autosomes
> for the time being.
>
> This is the error message I get now:
>
> > seg <- anomSegmentBAF(blData, genoData, scan.ids=scan.ids,
> + chrom.ids=chrom.ids, snp.ids=snp.ids)
> Error in anomSegmentBAF(blData, genoData, scan.ids = scan.ids, chrom.ids
> = chrom.ids, :
> no valid BAF values for chromosomes in chrom.ids
>
> Hopefully this helps.
>
> Best,
> Sam
>
>
> On Tue, Jun 4, 2013 at 12:28 AM, Stephanie M. Gogarten
> <sdmorris at u.washington.edu <mailto:sdmorris at u.washington.edu>> wrote:
>
> You have only one sample in your netCDF files - is this intentional?
>
> That should not cause your error, however. Can you try running with
> the latest GWASTools version and tell me what the new error message is?
>
> Also, you should include in your scan annotation a character vector
> "sex" with values of "M" or "F". The code treats males and females
> differently for X chromosome SNPs, and will complain later if this
> variable is missing.
>
> Stephanie
>
>
> On 6/3/13 4:04 PM, Sam Rose wrote:
>
> After checking again it still isn't quite working.
>
> I am pasting below the str() results for my intensity and genotype
> objects, maybe something in this can point clearly to what I am
> doing
> wrong.
>
> I am using an integer vector of 1 to the total number of snps
> for my snp
> id since it gave me some trouble before when it wasn't sorted.
>
> Best,
> Sam
>
> > str(genoData)
> Formal class 'GenotypeData' [package "GWASTools"] with 3 slots
> ..@ data :Formal class 'NcdfGenotypeReader' [package
> "GWASTools"]
> with 13 slots
> .. .. ..@ snpDim : chr "snp"
> .. .. ..@ scanDim : chr "sample"
> .. .. ..@ snpIDvar : chr "snp"
> .. .. ..@ chromosomeVar: chr "chromosome"
> .. .. ..@ positionVar : chr "position"
> .. .. ..@ scanIDvar : chr "sampleID"
> .. .. ..@ genotypeVar : chr "genotype"
> .. .. ..@ XchromCode : int 23
> .. .. ..@ YchromCode : int 25
> .. .. ..@ XYchromCode : int 24
> .. .. ..@ MchromCode : int 26
> .. .. ..@ filename : chr "tmp.geno.skea.nc
> <http://tmp.geno.skea.nc> <http://tmp.geno.skea.nc>"
>
> .. .. ..@ handler :List of 10
> .. .. .. ..$ id : int 524288
> .. .. .. ..$ ndims : int 2
> .. .. .. ..$ natts : int 2
> .. .. .. ..$ unlimdimid : num 1
> .. .. .. ..$ filename : chr "tmp.geno.skea.nc
> <http://tmp.geno.skea.nc>
> <http://tmp.geno.skea.nc>"
>
> .. .. .. ..$ varid2Rindex: num [1:6] 0 1 0 2 3 4
> .. .. .. ..$ writable : logi FALSE
> .. .. .. ..$ dim :List of 2
> .. .. .. .. ..$ sample:List of 8
> .. .. .. .. .. ..$ name : chr "sample"
> .. .. .. .. .. ..$ len : int 1
> .. .. .. .. .. ..$ unlim : logi TRUE
> .. .. .. .. .. ..$ id : int 1
> .. .. .. .. .. ..$ dimvarid : num 1
> .. .. .. .. .. ..$ units : chr "count"
> .. .. .. .. .. ..$ vals : logi NA
> .. .. .. .. .. ..$ create_dimvar: logi TRUE
> .. .. .. .. .. ..- attr(*, "class")= chr "dim.ncdf"
> .. .. .. .. ..$ snp :List of 8
> .. .. .. .. .. ..$ name : chr "snp"
> .. .. .. .. .. ..$ len : int 709358
> .. .. .. .. .. ..$ unlim : logi FALSE
> .. .. .. .. .. ..$ id : int 2
> .. .. .. .. .. ..$ dimvarid : num 3
> .. .. .. .. .. ..$ units : chr "count"
> .. .. .. .. .. ..$ vals : int [1:709358(1d)] 1 2 3 4
> 5 6 7 8
> 9 10 ...
> .. .. .. .. .. ..$ create_dimvar: logi TRUE
> .. .. .. .. .. ..- attr(*, "class")= chr "dim.ncdf"
> .. .. .. ..$ nvars : num 4
> .. .. .. ..$ var :List of 4
> .. .. .. .. ..$ sampleID :List of 16
> .. .. .. .. .. ..$ id : int 2
> .. .. .. .. .. ..$ name : chr "sampleID"
> .. .. .. .. .. ..$ ndims : int 1
> .. .. .. .. .. ..$ natts : int 2
> .. .. .. .. .. ..$ size : int 1
> .. .. .. .. .. ..$ prec : chr "int"
> .. .. .. .. .. ..$ dimids : num 1
> .. .. .. .. .. ..$ units : chr "id"
> .. .. .. .. .. ..$ longname : chr "sampleID"
> .. .. .. .. .. ..$ dims : list()
> .. .. .. .. .. ..$ dim :List of 1
> .. .. .. .. .. .. ..$ :List of 8
> .. .. .. .. .. .. .. ..$ name : chr "sample"
> .. .. .. .. .. .. .. ..$ len : int 1
> .. .. .. .. .. .. .. ..$ unlim : logi TRUE
> .. .. .. .. .. .. .. ..$ id : int 1
> .. .. .. .. .. .. .. ..$ dimvarid : num 1
> .. .. .. .. .. .. .. ..$ units : chr "count"
> .. .. .. .. .. .. .. ..$ vals : logi NA
> .. .. .. .. .. .. .. ..$ create_dimvar: logi TRUE
> .. .. .. .. .. .. .. ..- attr(*, "class")= chr "dim.ncdf"
> .. .. .. .. .. ..$ varsize : int 1
> .. .. .. .. .. ..$ unlim : logi TRUE
> .. .. .. .. .. ..$ missval : int 0
> .. .. .. .. .. ..$ hasAddOffset: logi FALSE
> .. .. .. .. .. ..$ hasScaleFact: logi FALSE
> .. .. .. .. .. ..- attr(*, "class")= chr "var.ncdf"
> .. .. .. .. ..$ position :List of 16
> .. .. .. .. .. ..$ id : int 4
> .. .. .. .. .. ..$ name : chr "position"
> .. .. .. .. .. ..$ ndims : int 1
> .. .. .. .. .. ..$ natts : int 2
> .. .. .. .. .. ..$ size : int 709358
> .. .. .. .. .. ..$ prec : chr "int"
> .. .. .. .. .. ..$ dimids : num 2
> .. .. .. .. .. ..$ units : chr "bases"
> .. .. .. .. .. ..$ longname : chr "position"
> .. .. .. .. .. ..$ dims : list()
> .. .. .. .. .. ..$ dim :List of 1
> .. .. .. .. .. .. ..$ :List of 8
> .. .. .. .. .. .. .. ..$ name : chr "snp"
> .. .. .. .. .. .. .. ..$ len : int 709358
> .. .. .. .. .. .. .. ..$ unlim : logi FALSE
> .. .. .. .. .. .. .. ..$ id : int 2
> .. .. .. .. .. .. .. ..$ dimvarid : num 3
> .. .. .. .. .. .. .. ..$ units : chr "count"
> .. .. .. .. .. .. .. ..$ vals : int [1:709358(1d)] 1
> 2 3 4 5
> 6 7 8 9 10 ...
> .. .. .. .. .. .. .. ..$ create_dimvar: logi TRUE
> .. .. .. .. .. .. .. ..- attr(*, "class")= chr "dim.ncdf"
> .. .. .. .. .. ..$ varsize : int 709358
> .. .. .. .. .. ..$ unlim : logi FALSE
> .. .. .. .. .. ..$ missval : int -1
> .. .. .. .. .. ..$ hasAddOffset: logi FALSE
> .. .. .. .. .. ..$ hasScaleFact: logi FALSE
> .. .. .. .. .. ..- attr(*, "class")= chr "var.ncdf"
> .. .. .. .. ..$ chromosome:List of 16
> .. .. .. .. .. ..$ id : int 5
> .. .. .. .. .. ..$ name : chr "chromosome"
> .. .. .. .. .. ..$ ndims : int 1
> .. .. .. .. .. ..$ natts : int 2
> .. .. .. .. .. ..$ size : int 709358
> .. .. .. .. .. ..$ prec : chr "int"
> .. .. .. .. .. ..$ dimids : num 2
> .. .. .. .. .. ..$ units : chr "id"
> .. .. .. .. .. ..$ longname : chr "chromosome"
> .. .. .. .. .. ..$ dims : list()
> .. .. .. .. .. ..$ dim :List of 1
> .. .. .. .. .. .. ..$ :List of 8
> .. .. .. .. .. .. .. ..$ name : chr "snp"
> .. .. .. .. .. .. .. ..$ len : int 709358
> .. .. .. .. .. .. .. ..$ unlim : logi FALSE
> .. .. .. .. .. .. .. ..$ id : int 2
> .. .. .. .. .. .. .. ..$ dimvarid : num 3
> .. .. .. .. .. .. .. ..$ units : chr "count"
> .. .. .. .. .. .. .. ..$ vals : int [1:709358(1d)] 1
> 2 3 4 5
> 6 7 8 9 10 ...
> .. .. .. .. .. .. .. ..$ create_dimvar: logi TRUE
> .. .. .. .. .. .. .. ..- attr(*, "class")= chr "dim.ncdf"
> .. .. .. .. .. ..$ varsize : int 709358
> .. .. .. .. .. ..$ unlim : logi FALSE
> .. .. .. .. .. ..$ missval : int -1
> .. .. .. .. .. ..$ hasAddOffset: logi FALSE
> .. .. .. .. .. ..$ hasScaleFact: logi FALSE
> .. .. .. .. .. ..- attr(*, "class")= chr "var.ncdf"
> .. .. .. .. ..$ genotype :List of 16
> .. .. .. .. .. ..$ id : int 6
> .. .. .. .. .. ..$ name : chr "genotype"
> .. .. .. .. .. ..$ ndims : int 2
> .. .. .. .. .. ..$ natts : int 2
> .. .. .. .. .. ..$ size : int [1:2] 709358 1
> .. .. .. .. .. ..$ prec : chr "byte"
> .. .. .. .. .. ..$ dimids : num [1:2] 2 1
> .. .. .. .. .. ..$ units : chr "num_A_alleles"
> .. .. .. .. .. ..$ longname : chr "genotype"
> .. .. .. .. .. ..$ dims : list()
> .. .. .. .. .. ..$ dim :List of 2
> .. .. .. .. .. .. ..$ :List of 8
> .. .. .. .. .. .. .. ..$ name : chr "snp"
> .. .. .. .. .. .. .. ..$ len : int 709358
> .. .. .. .. .. .. .. ..$ unlim : logi FALSE
> .. .. .. .. .. .. .. ..$ id : int 2
> .. .. .. .. .. .. .. ..$ dimvarid : num 3
> .. .. .. .. .. .. .. ..$ units : chr "count"
> .. .. .. .. .. .. .. ..$ vals : int [1:709358(1d)] 1
> 2 3 4 5
> 6 7 8 9 10 ...
> .. .. .. .. .. .. .. ..$ create_dimvar: logi TRUE
> .. .. .. .. .. .. .. ..- attr(*, "class")= chr "dim.ncdf"
> .. .. .. .. .. .. ..$ :List of 8
> .. .. .. .. .. .. .. ..$ name : chr "sample"
> .. .. .. .. .. .. .. ..$ len : int 1
> .. .. .. .. .. .. .. ..$ unlim : logi TRUE
> .. .. .. .. .. .. .. ..$ id : int 1
> .. .. .. .. .. .. .. ..$ dimvarid : num 1
> .. .. .. .. .. .. .. ..$ units : chr "count"
> .. .. .. .. .. .. .. ..$ vals : logi NA
> .. .. .. .. .. .. .. ..$ create_dimvar: logi TRUE
> .. .. .. .. .. .. .. ..- attr(*, "class")= chr "dim.ncdf"
> .. .. .. .. .. ..$ varsize : int [1:2] 709358 1
> .. .. .. .. .. ..$ unlim : logi TRUE
> .. .. .. .. .. ..$ missval : int -1
> .. .. .. .. .. ..$ hasAddOffset: logi FALSE
> .. .. .. .. .. ..$ hasScaleFact: logi FALSE
> .. .. .. .. .. ..- attr(*, "class")= chr "var.ncdf"
> .. .. .. ..- attr(*, "class")= chr "ncdf"
> ..@ snpAnnot :Formal class 'SnpAnnotationDataFrame' [package
> "GWASTools"] with 11 slots
> .. .. ..@ idCol : chr "snpID"
> .. .. ..@ chromosomeCol : chr "chromosome"
> .. .. ..@ positionCol : chr "position"
> .. .. ..@ XchromCode : int 23
> .. .. ..@ YchromCode : int 25
> .. .. ..@ XYchromCode : int 24
> .. .. ..@ MchromCode : int 26
> .. .. ..@ varMetadata :'data.frame': 4 obs. of 1
> variable:
> .. .. .. ..$ labelDescription: chr [1:4] NA NA NA NA
> .. .. ..@ data :'data.frame': 709358 obs. of 4
> variables:
> .. .. .. ..$ snpID : int [1:709358] 1 2 3 4 5 6 7 8 9 10 ...
> .. .. .. ..$ chromosome: int [1:709358] 1 1 1 1 1 1 1 1 1 1 ...
> .. .. .. ..$ position : int [1:709358] 82154 752566 752721
> 768448
> 776546 798959 800007 838555 846808 854250 ...
> .. .. .. ..$ rsID : Factor w/ 709358 levels
> "rs1000000","rs1000002",..: 444820 394558 397236 154397 130894 89309
> 528142 485618 444755 595849 ...
> .. .. ..@ dimLabels : chr [1:2] "snps" "variables"
> .. .. ..@ .__classVersion__:Formal class 'Versions' [package
> "Biobase"] with 1 slots
> .. .. .. .. ..@ .Data:List of 1
> .. .. .. .. .. ..$ : int [1:3] 1 1 0
> ..@ scanAnnot:Formal class 'ScanAnnotationDataFrame' [package
> "GWASTools"] with 6 slots
> .. .. ..@ idCol : chr "scanID"
> .. .. ..@ sexCol : chr "sex"
> .. .. ..@ varMetadata :'data.frame': 4 obs. of 1
> variable:
> .. .. .. ..$ labelDescription: chr [1:4] NA NA NA NA
> .. .. ..@ data :'data.frame': 1 obs. of 4
> variables:
> .. .. .. ..$ scanID : int 1
> .. .. .. ..$ subjectID: Factor w/ 1 level "PT-PTWN": 1
> .. .. .. ..$ genoRunID: Factor w/ 1 level "8820505004_R01C01": 1
> .. .. .. ..$ file : Factor w/ 1 level
> "8820505004_R01C01.gtc.txt.__use": 1
> .. .. ..@ dimLabels : chr [1:2] "scans" "variables"
> .. .. ..@ .__classVersion__:Formal class 'Versions' [package
> "Biobase"] with 1 slots
> .. .. .. .. ..@ .Data:List of 1
> .. .. .. .. .. ..$ : int [1:3] 1 1 0
>
> > str(blData)
> Formal class 'IntensityData' [package "GWASTools"] with 3 slots
> ..@ data :Formal class 'NcdfIntensityReader' [package
> "GWASTools"] with 17 slots
> .. .. ..@ snpDim : chr "snp"
> .. .. ..@ scanDim : chr "sample"
> .. .. ..@ snpIDvar : chr "snp"
> .. .. ..@ chromosomeVar: chr "chromosome"
> .. .. ..@ positionVar : chr "position"
> .. .. ..@ scanIDvar : chr "sampleID"
> .. .. ..@ qualityVar : chr "quality"
> .. .. ..@ xVar : chr "X"
> .. .. ..@ yVar : chr "Y"
> .. .. ..@ bafVar : chr "BAlleleFreq"
> .. .. ..@ lrrVar : chr "LogRRatio"
> .. .. ..@ XchromCode : int 23
> .. .. ..@ YchromCode : int 25
> .. .. ..@ XYchromCode : int 24
> .. .. ..@ MchromCode : int 26
> .. .. ..@ filename : chr "tmp.baf.skea.nc
> <http://tmp.baf.skea.nc> <http://tmp.baf.skea.nc>"
>
> .. .. ..@ handler :List of 10
> .. .. .. ..$ id : int 458752
> .. .. .. ..$ ndims : int 2
> .. .. .. ..$ natts : int 2
> .. .. .. ..$ unlimdimid : num 1
> .. .. .. ..$ filename : chr "tmp.baf.skea.nc
> <http://tmp.baf.skea.nc> <http://tmp.baf.skea.nc>"
>
> .. .. .. ..$ varid2Rindex: num [1:7] 0 1 0 2 3 4 5
> .. .. .. ..$ writable : logi FALSE
> .. .. .. ..$ dim :List of 2
> .. .. .. .. ..$ sample:List of 8
> .. .. .. .. .. ..$ name : chr "sample"
> .. .. .. .. .. ..$ len : int 1
> .. .. .. .. .. ..$ unlim : logi TRUE
> .. .. .. .. .. ..$ id : int 1
> .. .. .. .. .. ..$ dimvarid : num 1
> .. .. .. .. .. ..$ units : chr "count"
> .. .. .. .. .. ..$ vals : logi NA
> .. .. .. .. .. ..$ create_dimvar: logi TRUE
> .. .. .. .. .. ..- attr(*, "class")= chr "dim.ncdf"
> .. .. .. .. ..$ snp :List of 8
> .. .. .. .. .. ..$ name : chr "snp"
> .. .. .. .. .. ..$ len : int 709358
> .. .. .. .. .. ..$ unlim : logi FALSE
> .. .. .. .. .. ..$ id : int 2
> .. .. .. .. .. ..$ dimvarid : num 3
> .. .. .. .. .. ..$ units : chr "count"
> .. .. .. .. .. ..$ vals : int [1:709358(1d)] 1 2 3 4
> 5 6 7 8
> 9 10 ...
> .. .. .. .. .. ..$ create_dimvar: logi TRUE
> .. .. .. .. .. ..- attr(*, "class")= chr "dim.ncdf"
> .. .. .. ..$ nvars : num 5
> .. .. .. ..$ var :List of 5
> .. .. .. .. ..$ sampleID :List of 16
> .. .. .. .. .. ..$ id : int 2
> .. .. .. .. .. ..$ name : chr "sampleID"
> .. .. .. .. .. ..$ ndims : int 1
> .. .. .. .. .. ..$ natts : int 2
> .. .. .. .. .. ..$ size : int 1
> .. .. .. .. .. ..$ prec : chr "int"
> .. .. .. .. .. ..$ dimids : num 1
> .. .. .. .. .. ..$ units : chr "id"
> .. .. .. .. .. ..$ longname : chr "sampleID"
> .. .. .. .. .. ..$ dims : list()
> .. .. .. .. .. ..$ dim :List of 1
> .. .. .. .. .. .. ..$ :List of 8
> .. .. .. .. .. .. .. ..$ name : chr "sample"
> .. .. .. .. .. .. .. ..$ len : int 1
> .. .. .. .. .. .. .. ..$ unlim : logi TRUE
> .. .. .. .. .. .. .. ..$ id : int 1
> .. .. .. .. .. .. .. ..$ dimvarid : num 1
> .. .. .. .. .. .. .. ..$ units : chr "count"
> .. .. .. .. .. .. .. ..$ vals : logi NA
> .. .. .. .. .. .. .. ..$ create_dimvar: logi TRUE
> .. .. .. .. .. .. .. ..- attr(*, "class")= chr "dim.ncdf"
> .. .. .. .. .. ..$ varsize : int 1
> .. .. .. .. .. ..$ unlim : logi TRUE
> .. .. .. .. .. ..$ missval : int 0
> .. .. .. .. .. ..$ hasAddOffset: logi FALSE
> .. .. .. .. .. ..$ hasScaleFact: logi FALSE
> .. .. .. .. .. ..- attr(*, "class")= chr "var.ncdf"
> .. .. .. .. ..$ position :List of 16
> .. .. .. .. .. ..$ id : int 4
> .. .. .. .. .. ..$ name : chr "position"
> .. .. .. .. .. ..$ ndims : int 1
> .. .. .. .. .. ..$ natts : int 2
> .. .. .. .. .. ..$ size : int 709358
> .. .. .. .. .. ..$ prec : chr "int"
> .. .. .. .. .. ..$ dimids : num 2
> .. .. .. .. .. ..$ units : chr "bases"
> .. .. .. .. .. ..$ longname : chr "position"
> .. .. .. .. .. ..$ dims : list()
> .. .. .. .. .. ..$ dim :List of 1
> .. .. .. .. .. .. ..$ :List of 8
> .. .. .. .. .. .. .. ..$ name : chr "snp"
> .. .. .. .. .. .. .. ..$ len : int 709358
> .. .. .. .. .. .. .. ..$ unlim : logi FALSE
> .. .. .. .. .. .. .. ..$ id : int 2
> .. .. .. .. .. .. .. ..$ dimvarid : num 3
> .. .. .. .. .. .. .. ..$ units : chr "count"
> .. .. .. .. .. .. .. ..$ vals : int [1:709358(1d)] 1
> 2 3 4 5
> 6 7 8 9 10 ...
> .. .. .. .. .. .. .. ..$ create_dimvar: logi TRUE
> .. .. .. .. .. .. .. ..- attr(*, "class")= chr "dim.ncdf"
> .. .. .. .. .. ..$ varsize : int 709358
> .. .. .. .. .. ..$ unlim : logi FALSE
> .. .. .. .. .. ..$ missval : int -1
> .. .. .. .. .. ..$ hasAddOffset: logi FALSE
> .. .. .. .. .. ..$ hasScaleFact: logi FALSE
> .. .. .. .. .. ..- attr(*, "class")= chr "var.ncdf"
> .. .. .. .. ..$ chromosome :List of 16
> .. .. .. .. .. ..$ id : int 5
> .. .. .. .. .. ..$ name : chr "chromosome"
> .. .. .. .. .. ..$ ndims : int 1
> .. .. .. .. .. ..$ natts : int 2
> .. .. .. .. .. ..$ size : int 709358
> .. .. .. .. .. ..$ prec : chr "int"
> .. .. .. .. .. ..$ dimids : num 2
> .. .. .. .. .. ..$ units : chr "id"
> .. .. .. .. .. ..$ longname : chr "chromosome"
> .. .. .. .. .. ..$ dims : list()
> .. .. .. .. .. ..$ dim :List of 1
> .. .. .. .. .. .. ..$ :List of 8
> .. .. .. .. .. .. .. ..$ name : chr "snp"
> .. .. .. .. .. .. .. ..$ len : int 709358
> .. .. .. .. .. .. .. ..$ unlim : logi FALSE
> .. .. .. .. .. .. .. ..$ id : int 2
> .. .. .. .. .. .. .. ..$ dimvarid : num 3
> .. .. .. .. .. .. .. ..$ units : chr "count"
> .. .. .. .. .. .. .. ..$ vals : int [1:709358(1d)] 1
> 2 3 4 5
> 6 7 8 9 10 ...
> .. .. .. .. .. .. .. ..$ create_dimvar: logi TRUE
> .. .. .. .. .. .. .. ..- attr(*, "class")= chr "dim.ncdf"
> .. .. .. .. .. ..$ varsize : int 709358
> .. .. .. .. .. ..$ unlim : logi FALSE
> .. .. .. .. .. ..$ missval : int -1
> .. .. .. .. .. ..$ hasAddOffset: logi FALSE
> .. .. .. .. .. ..$ hasScaleFact: logi FALSE
> .. .. .. .. .. ..- attr(*, "class")= chr "var.ncdf"
> .. .. .. .. ..$ BAlleleFreq:List of 16
> .. .. .. .. .. ..$ id : int 6
> .. .. .. .. .. ..$ name : chr "BAlleleFreq"
> .. .. .. .. .. ..$ ndims : int 2
> .. .. .. .. .. ..$ natts : int 2
> .. .. .. .. .. ..$ size : int [1:2] 709358 1
> .. .. .. .. .. ..$ prec : chr "float"
> .. .. .. .. .. ..$ dimids : num [1:2] 2 1
> .. .. .. .. .. ..$ units : chr "intensity"
> .. .. .. .. .. ..$ longname : chr "BAlleleFreq"
> .. .. .. .. .. ..$ dims : list()
> .. .. .. .. .. ..$ dim :List of 2
> .. .. .. .. .. .. ..$ :List of 8
> .. .. .. .. .. .. .. ..$ name : chr "snp"
> .. .. .. .. .. .. .. ..$ len : int 709358
> .. .. .. .. .. .. .. ..$ unlim : logi FALSE
> .. .. .. .. .. .. .. ..$ id : int 2
> .. .. .. .. .. .. .. ..$ dimvarid : num 3
> .. .. .. .. .. .. .. ..$ units : chr "count"
> .. .. .. .. .. .. .. ..$ vals : int [1:709358(1d)] 1
> 2 3 4 5
> 6 7 8 9 10 ...
> .. .. .. .. .. .. .. ..$ create_dimvar: logi TRUE
> .. .. .. .. .. .. .. ..- attr(*, "class")= chr "dim.ncdf"
> .. .. .. .. .. .. ..$ :List of 8
> .. .. .. .. .. .. .. ..$ name : chr "sample"
> .. .. .. .. .. .. .. ..$ len : int 1
> .. .. .. .. .. .. .. ..$ unlim : logi TRUE
> .. .. .. .. .. .. .. ..$ id : int 1
> .. .. .. .. .. .. .. ..$ dimvarid : num 1
> .. .. .. .. .. .. .. ..$ units : chr "count"
> .. .. .. .. .. .. .. ..$ vals : logi NA
> .. .. .. .. .. .. .. ..$ create_dimvar: logi TRUE
> .. .. .. .. .. .. .. ..- attr(*, "class")= chr "dim.ncdf"
> .. .. .. .. .. ..$ varsize : int [1:2] 709358 1
> .. .. .. .. .. ..$ unlim : logi TRUE
> .. .. .. .. .. ..$ missval : num -9999
> .. .. .. .. .. ..$ hasAddOffset: logi FALSE
> .. .. .. .. .. ..$ hasScaleFact: logi FALSE
> .. .. .. .. .. ..- attr(*, "class")= chr "var.ncdf"
> .. .. .. .. ..$ LogRRatio :List of 16
> .. .. .. .. .. ..$ id : int 7
> .. .. .. .. .. ..$ name : chr "LogRRatio"
> .. .. .. .. .. ..$ ndims : int 2
> .. .. .. .. .. ..$ natts : int 2
> .. .. .. .. .. ..$ size : int [1:2] 709358 1
> .. .. .. .. .. ..$ prec : chr "float"
> .. .. .. .. .. ..$ dimids : num [1:2] 2 1
> .. .. .. .. .. ..$ units : chr "intensity"
> .. .. .. .. .. ..$ longname : chr "LogRRatio"
> .. .. .. .. .. ..$ dims : list()
> .. .. .. .. .. ..$ dim :List of 2
> .. .. .. .. .. .. ..$ :List of 8
> .. .. .. .. .. .. .. ..$ name : chr "snp"
> .. .. .. .. .. .. .. ..$ len : int 709358
> .. .. .. .. .. .. .. ..$ unlim : logi FALSE
> .. .. .. .. .. .. .. ..$ id : int 2
> .. .. .. .. .. .. .. ..$ dimvarid : num 3
> .. .. .. .. .. .. .. ..$ units : chr "count"
> .. .. .. .. .. .. .. ..$ vals : int [1:709358(1d)] 1
> 2 3 4 5
> 6 7 8 9 10 ...
> .. .. .. .. .. .. .. ..$ create_dimvar: logi TRUE
> .. .. .. .. .. .. .. ..- attr(*, "class")= chr "dim.ncdf"
> .. .. .. .. .. .. ..$ :List of 8
> .. .. .. .. .. .. .. ..$ name : chr "sample"
> .. .. .. .. .. .. .. ..$ len : int 1
> .. .. .. .. .. .. .. ..$ unlim : logi TRUE
> .. .. .. .. .. .. .. ..$ id : int 1
> .. .. .. .. .. .. .. ..$ dimvarid : num 1
> .. .. .. .. .. .. .. ..$ units : chr "count"
> .. .. .. .. .. .. .. ..$ vals : logi NA
> .. .. .. .. .. .. .. ..$ create_dimvar: logi TRUE
> .. .. .. .. .. .. .. ..- attr(*, "class")= chr "dim.ncdf"
> .. .. .. .. .. ..$ varsize : int [1:2] 709358 1
> .. .. .. .. .. ..$ unlim : logi TRUE
> .. .. .. .. .. ..$ missval : num -9999
> .. .. .. .. .. ..$ hasAddOffset: logi FALSE
> .. .. .. .. .. ..$ hasScaleFact: logi FALSE
> .. .. .. .. .. ..- attr(*, "class")= chr "var.ncdf"
> .. .. .. ..- attr(*, "class")= chr "ncdf"
> ..@ snpAnnot :Formal class 'SnpAnnotationDataFrame' [package
> "GWASTools"] with 11 slots
> .. .. ..@ idCol : chr "snpID"
> .. .. ..@ chromosomeCol : chr "chromosome"
> .. .. ..@ positionCol : chr "position"
> .. .. ..@ XchromCode : int 23
> .. .. ..@ YchromCode : int 25
> .. .. ..@ XYchromCode : int 24
> .. .. ..@ MchromCode : int 26
> .. .. ..@ varMetadata :'data.frame': 4 obs. of 1
> variable:
> .. .. .. ..$ labelDescription: chr [1:4] NA NA NA NA
> .. .. ..@ data :'data.frame': 709358 obs. of 4
> variables:
> .. .. .. ..$ snpID : int [1:709358] 1 2 3 4 5 6 7 8 9 10 ...
> .. .. .. ..$ chromosome: int [1:709358] 1 1 1 1 1 1 1 1 1 1 ...
> .. .. .. ..$ position : int [1:709358] 82154 752566 752721
> 768448
> 776546 798959 800007 838555 846808 854250 ...
> .. .. .. ..$ rsID : Factor w/ 709358 levels
> "rs1000000","rs1000002",..: 444820 394558 397236 154397 130894 89309
> 528142 485618 444755 595849 ...
> .. .. ..@ dimLabels : chr [1:2] "snps" "variables"
> .. .. ..@ .__classVersion__:Formal class 'Versions' [package
> "Biobase"] with 1 slots
> .. .. .. .. ..@ .Data:List of 1
> .. .. .. .. .. ..$ : int [1:3] 1 1 0
> ..@ scanAnnot:Formal class 'ScanAnnotationDataFrame' [package
> "GWASTools"] with 6 slots
> .. .. ..@ idCol : chr "scanID"
> .. .. ..@ sexCol : chr "sex"
> .. .. ..@ varMetadata :'data.frame': 4 obs. of 1
> variable:
> .. .. .. ..$ labelDescription: chr [1:4] NA NA NA NA
> .. .. ..@ data :'data.frame': 1 obs. of 4
> variables:
> .. .. .. ..$ scanID : int 1
> .. .. .. ..$ subjectID: Factor w/ 1 level "PT-PTWN": 1
> .. .. .. ..$ genoRunID: Factor w/ 1 level "8820505004_R01C01": 1
> .. .. .. ..$ file : Factor w/ 1 level
> "8820505004_R01C01.gtc.txt.__use": 1
> .. .. ..@ dimLabels : chr [1:2] "scans" "variables"
> .. .. ..@ .__classVersion__:Formal class 'Versions' [package
> "Biobase"] with 1 slots
> .. .. .. .. ..@ .Data:List of 1
> .. .. .. .. .. ..$ : int [1:3] 1 1 0
>
>
>
> On Fri, May 31, 2013 at 2:41 PM, Sam Rose
> <srose at broadinstitute.org <mailto:srose at broadinstitute.org>
> <mailto:srose at broadinstitute.__org
> <mailto:srose at broadinstitute.org>>> wrote:
>
> Looks like there was some problems reading the file in on
> my end,
> some chromosomes didn't make it in probably from a
> preprocessing
> step on my end. I'll let you know if I can't rectify.
>
> Thanks again for the help,
>
> Sam
>
>
> On Thu, May 30, 2013 at 4:43 PM, Stephanie M. Gogarten
> <sdmorris at u.washington.edu
> <mailto:sdmorris at u.washington.edu>
> <mailto:sdmorris at u.washington.__edu
> <mailto:sdmorris at u.washington.edu>>> wrote:
>
> Hi Sam,
>
> I need to add a more informative error message - the
> problem is
> that no valid BAF values are reaching the call to CNA
> (baf.dat
> is NULL). This could happen if the values of snp.ids or
> chrom.ids are invalid - these should all be integer values
> matching the contents of snpID and chromosome in the netCDF
> file. What values are you using for these arguments?
>
> You will need to have LRR in the intensity NetCDF file. A
> portion of the code downstream from the error you're
> getting
> uses LRR to filter potential anomalies.
>
> Stephanie
>
>
> On 5/30/13 12:30 PM, Sam Rose wrote:
>
> Thank you for your previous help Stephanie.
>
> I am afraid I have another problem I can't seem to
> work out.
>
> I have gotten as far as reading in the BAlleleFreq
> and Geno
> files into
> their respective ncdf formats. I only have the baf
> data in
> the intensity
> ncdf file, do I need LRR too? When I run the
> anomDetectBAF()
> function it
> gives me this error:
>
> > anom <- anomDetectBAF(blData, genoData,
> scan.ids=scan.ids,
> chrom.ids=chrom.ids, snp.ids=snp.ids,
> centromere=centromeres.hg19)
> Error in CNA(as.vector(baf.dat), chr, index,
> data.type =
> "logratio",
> sampleid = snum) :
> genomdat must be numeric
>
> I have checked and the data that I put in to the
> genotype
> data file was
> numeric and present as well as the baf data. I'm
> wondering
> if you have
> seen this error before and may potentially know
> what I can
> do to rectify?
>
> Thanks,
> Sam
>
>
> On Wed, Apr 24, 2013 at 12:01 AM, Stephanie M. Gogarten
> <sdmorris at u.washington.edu
> <mailto:sdmorris at u.washington.edu>
> <mailto:sdmorris at u.washington.__edu
> <mailto:sdmorris at u.washington.edu>>
> <mailto:sdmorris at u.washington.
> <mailto:sdmorris at u.washington.>____edu
>
> <mailto:sdmorris at u.washington.__edu
> <mailto:sdmorris at u.washington.edu>>>> wrote:
>
> Hi Sam,
>
> Section 2 of the vignette "GWAS Data Cleaning"
> contains
> an example
> of how to import raw illumina data of exactly
> this type
> into
> GWASTools. The example data is contained in
> the package
> "GWASdata."
>
> If you have any further questions after
> reading the
> vignette, please
> cc the bioconductor mailing list
> (bioconductor at r-project.org
> <mailto:bioconductor at r-project.org>
> <mailto:bioconductor at r-__project.org
> <mailto:bioconductor at r-project.org>>
> <mailto:bioconductor at r-____project.org
> <mailto:bioconductor at r-__project.org>
>
> <mailto:bioconductor at r-__project.org
> <mailto:bioconductor at r-project.org>>>).
>
>
> Section 7 may also be of use to you, as it
> deals with
> chromosome
> anomaly detection.
>
> best wishes,
> Stephanie
>
>
> On 4/23/13 7:54 PM, Sam Rose wrote:
>
> Hi Stephanie,
>
> My name is Sam Rose and I am contacting
> you the
> GWASTools package in
> Bioconductor of which it says you are the
> maintainer.
>
> I am trying to use the package to call
> mosaic CNVs
> in my samples and
> can't seem to get it to work.
>
> I'm wondering if you have an example of
> the raw
> illumina data to
> put in
> there, and maybe examples of some of the
> things
> required in the
> 'ncdfAddData' command (i.e. sample column,
> col.nums). I have
> created the
> shell ncdf file, but beyond that the
> headers and
> data formats
> seem to be
> giving me trouble so I just though I would
> ask.
>
> Our Illumina raw data files look like this:
>
>
> SNP_NameChromosomePositionGC_______ScoreAllele1_-_TopAllele2_-_______TopAllele1_-_ABAllele2_-_______ABXYRaw_XRaw_YR___IlluminaTheta_______IlluminabAllele_FreqLog_R_______Ratio_IlluminaR_TrigTheta_______TrigLog_R_Ratio_Trig
>
>
> rs44772121720170.______38423407AAAA0.______393692269026780450.______0250181864147452338333240.______41871045544152570.______040401312884379780.______006063504097364059-0.______6120798296992830.______394486390567453940.______06346223387647508-0.______6182450719587295
>
>
>
> Thanks for your help,
>
> Sam
>
> --
> -----
> *Sam Rose, Stanley Center Research
> Associate II
>
> Stanley Center for Psychiatric Research,
> The Broad
> Institute
> 7 Cambridge Center, Cambridge, MA 02142*
> 617.714.7853, srose at broadinstitute.org
> <mailto:srose at broadinstitute.org>
> <mailto:srose at broadinstitute.__org
> <mailto:srose at broadinstitute.org>>
> <mailto:srose at broadinstitute.
> <mailto:srose at broadinstitute.>____org
> <mailto:srose at broadinstitute.__org
> <mailto:srose at broadinstitute.org>>>
> <mailto:srose at broadinstitute
> <mailto:srose at broadinstitute>.
> <mailto:srose at broadinstitute
> <mailto:srose at broadinstitute>.>______org
>
> <mailto:srose at broadinstitute.
> <mailto:srose at broadinstitute.>____org
> <mailto:srose at broadinstitute.__org
> <mailto:srose at broadinstitute.org>>>>
>
>
>
>
>
> --
> -----
> *Sam Rose, Stanley Center Research Associate II
> Stanley Center for Psychiatric Research, The Broad
> Institute
> 7 Cambridge Center, Cambridge, MA 02142*
> 617.714.7853, srose at broadinstitute.org
> <mailto:srose at broadinstitute.org>
> <mailto:srose at broadinstitute.__org
> <mailto:srose at broadinstitute.org>>
> <mailto:srose at broadinstitute.
> <mailto:srose at broadinstitute.>____org
> <mailto:srose at broadinstitute.__org
> <mailto:srose at broadinstitute.org>>>
>
>
>
>
> --
> -----
>
> *Sam Rose, Stanley Center Research Associate II
> Stanley Center for Psychiatric Research, The Broad Institute
> 7 Cambridge Center, Cambridge, MA 02142*
> 617.714.7853, srose at broadinstitute.org
> <mailto:srose at broadinstitute.org>
> <mailto:srose at broadinstitute.__org
> <mailto:srose at broadinstitute.org>>
>
>
>
>
> --
> -----
> *Sam Rose, Stanley Center Research Associate II
> Stanley Center for Psychiatric Research, The Broad Institute
> 7 Cambridge Center, Cambridge, MA 02142*
> 617.714.7853, srose at broadinstitute.org
> <mailto:srose at broadinstitute.org>
> <mailto:srose at broadinstitute.__org
> <mailto:srose at broadinstitute.org>>
>
>
>
>
> --
> -----
> *Sam Rose, Stanley Center Research Associate II
> Stanley Center for Psychiatric Research, The Broad Institute
> 7 Cambridge Center, Cambridge, MA 02142*
> 617.714.7853, srose at broadinstitute.org <mailto:srose at broadinstitute.org>
>
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