[BioC] GWATools use in creating ncdf files
Stephanie M. Gogarten
sdmorris at u.washington.edu
Fri Jun 7 21:27:36 CEST 2013
Hi Sam,
I can't reproduce your error using the data you sent. Either you had an
error in creating your netCDF files, or the sample you were working with
doesn't have any usable data. Below is the code I used; see if you can
reproduce it with your other sample.
library(GWASTools)
scan.annot <- read.table("8850270138_R01C01.gtc.txt.scan_annotation",
colClasses=c("integer", rep("character",4)),
header=TRUE)
scanAnnot <- ScanAnnotationDataFrame(scan.annot)
snp.annot <- read.table("8850270138_R01C01.gtc.txt.snp_annotation",
as.is=TRUE, header=TRUE)
snpAnnot <- SnpAnnotationDataFrame(snp.annot)
geno.nc.file <- "geno.nc"
ncdfCreate(ncdf.filename=geno.nc.file, snp.annotation=snp.annot,
variables="genotype", n.samples=1, precision="single")
names(scan.annot)[3] <- "scanName"
names(snp.annot)[4] <- "snpName"
col.nums <- as.integer(c(1,7,8))
names(col.nums) <- c("snp","a1","a2")
ncdfAddData(path=".", ncdf.filename=geno.nc.file,
snp.annotation=snp.annot,
scan.annotation=scan.annot,
sep.type="\t", skip.num=1,
col.total=16, col.nums=col.nums,
scan.name.in.file=0)
bl.nc.file <- "bl.nc"
ncdfCreate(ncdf.filename=bl.nc.file, snp.annotation=snp.annot,
variables=c("BAlleleFreq", "LogRRatio"),
n.samples=1, precision="single")
col.nums <- as.integer(c(1,15,16))
names(col.nums) <- c("snp", "ballelefreq", "logrratio")
ncdfAddData(path=".", ncdf.filename=bl.nc.file,
snp.annotation=snp.annot,
scan.annotation=scan.annot,
sep.type="\t", skip.num=1,
col.total=16, col.nums=col.nums,
scan.name.in.file=0)
genoData <- GenotypeData(NcdfGenotypeReader(geno.nc.file),
scanAnnot=scanAnnot, snpAnnot=snpAnnot)
blData <- IntensityData(NcdfIntensityReader(bl.nc.file),
scanAnnot=scanAnnot, snpAnnot=snpAnnot)
scan.ids <- read.table("scan.ids")[,1]
snp.ids <- read.table("snp.ids")[,1]
chrom.ids <- read.table("chrom.ids")[,1]
seg <- anomSegmentBAF(blData, genoData, scan.ids=scan.ids,
chrom.ids=chrom.ids, snp.ids=snp.ids)
head(seg)
scanID chromosome left.index right.index num.mark seg.mean
1 1 1 5 59479 17205 0.1582
2 1 2 59498 117436 17360 0.1596
3 1 3 117437 164865 14181 0.1595
4 1 4 164872 205472 12218 0.1640
5 1 5 205474 247715 13313 0.1602
6 1 6 247752 296212 15232 0.1629
best wishes,
Stephanie
On 6/6/13 1:28 PM, Sam Rose wrote:
> Hi Stephanie,
>
> I am providing a CEU control sample data from the same study, NA12878. I
> just sent it to you in a dropbox link. Let me know if there are any
> questions.
>
> Best,
> Sam
>
>
>
>
> On Wed, Jun 5, 2013 at 12:11 PM, Stephanie M. Gogarten
> <sdmorris at u.washington.edu <mailto:sdmorris at u.washington.edu>> wrote:
>
> 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>
> <mailto: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> <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>
> <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> <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> <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>>
> <mailto:srose at broadinstitute.
> <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>>
> <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,
>
> 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>>>
> <mailto:sdmorris at u.washington
> <mailto:sdmorris at u.washington>.
> <mailto:sdmorris at u.washington
> <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>>>
>
> <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
> <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>>>>
> <mailto:srose at broadinstitute
> <mailto:srose at broadinstitute>
> <mailto:srose at broadinstitute
> <mailto:srose at broadinstitute>>.
> <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>.
> <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>>>
> <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>>
> <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>
>
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