Entering edit mode
Stephanie M. Gogarten
▴
870
@stephanie-m-gogarten-5121
Last seen 4 months ago
University of Washington
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="">"
> .. .. ..@ 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="">"
> .. .. .. ..$ 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="">"
> .. .. ..@ 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="">"
> .. .. .. ..$ 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="">> 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="">> 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="">>> 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="">>).
>
>
> 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_Illumin
aTheta_____IlluminabAllele_FreqLog_R_____Ratio_IlluminaR_TrigTheta____
_TrigLog_R_Ratio_Trig
>
> rs44772121720170.____38423407AAAA0.____39369226902678045
0.____0250181864147452338333240.____41871045544152570.____040401312884
379780.____006063504097364059-0.____6120798296992830.____3944863905674
53940.____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="">>>
>
>
>
>
>
> --
> -----
> *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="">
>
>
>
>
> --
> -----
> *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="">
>
