Entering edit mode
Sam Rose
▴
60
@sam-rose-5964
Last seen 10.2 years ago
Hi Stephanie,
Quick question, do you have any experience with the following error in
the
ncdfAddData() function?
Error in `[.data.frame`(dat, , new.names) : undefined columns selected
> traceback()
4: stop("undefined columns selected")
3: `[.data.frame`(dat, , new.names)
2: dat[, new.names]
1: 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)
I am using a new data set exactly the same as the last one which
worked and
can't seem to figure out the problem behind this one.
These are what the tops of my scan and snp annotation files look like:
snp:
snpID chromosome position rsID
1 1 72017 rs4477212
2 1 524110 SNP1-524110
3 1 555149 SNP1-555149
4 1 559487 SNP1-559487
5 1 679049 rs4000335
6 1 713781 SNP1-713781
7 1 719495 SNP1-719495
8 1 742429 rs3094315
9 1 742584 rs3131972
scan:
scanID subjectID genoRunID sex file
2 PT-JOPP 5491005008_R03C01 M
5491005008_R03C01.gtc.txt.use
3 PT-JOQ4 5434246116_R01C01 F
5434246116_R01C01.gtc.txt.use
4 PT-JOQ6 5491005134_R03C01 M
5491005134_R03C01.gtc.txt.use
5 PT-JOQB 5434078047_R04C01 F
5434078047_R04C01.gtc.txt.use
6 PT-JOQG 5491005152_R03C01 F
5491005152_R03C01.gtc.txt.use
7 PT-JOP2 5434246116_R03C01 F
5434246116_R03C01.gtc.txt.use
8 PT-JOQI 5491005134_R04C01 M
5491005134_R04C01.gtc.txt.use
9 PT-JOQL 5434246084_R04C01 M
5434246084_R04C01.gtc.txt.use
11 PT-JOQW 5491005061_R02C01 M
5491005061_R02C01.gtc.txt.use
Any help would be appreciated.
Thanks,
Sam
On Wed, Jun 12, 2013 at 9:45 AM, Sam Rose <srose@broadinstitute.org>
wrote:
> Hi Stephanie,
>
> After using your commands I was able to successfully use the package
> without error. I think the error was within the column names, which
needed
> to be changed from genoRunID to scanID in order to be recognized by
the
> later commands.
>
> Thanks for all of your help it was very much appreciated.
>
> Best,
> Sam
>
>
> On Fri, Jun 7, 2013 at 3:27 PM, Stephanie M. Gogarten <
> sdmorris@u.washington.edu> wrote:
>
>> 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(**NcdfGenotypeReadergeno.nc.**file),
>> scanAnnot=scanAnnot, snpAnnot=snpAnnot)
>> blData <- IntensityData(**NcdfIntensityReaderbl.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@u.washington.edu <mailto:sdmorris@u.washington.**edu<sdmorris@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@u.washington.edu <mailto:sdmorris@u.washington.**edu<sdmorris@u.washington.edu="">
>>> >
>>> <mailto:sdmorris@u.washington.**__edu>>> <mailto:sdmorris@u.washington.**edu <sdmorris@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@broadinstitute.org>>> <mailto:srose@broadinstitute.**org <srose@broadinstitute.org="">>
>>> <mailto:srose@broadinstitute._**_org>>> <mailto:srose@broadinstitute.**org <srose@broadinstitute.org="">>>
>>> <mailto:srose@broadinstitute.>>> <mailto:srose@broadinstitute.>**____org
>>>
>>> <mailto:srose@broadinstitute._**_org>>> <mailto:srose@broadinstitute.**org <srose@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@u.washington.edu>>> <mailto:sdmorris@u.washington.**edu <sdmorris@u.washington.edu="">>
>>> <mailto:sdmorris@u.washington.**__edu>>> <mailto:sdmorris@u.washington.**edu <sdmorris@u.washington.edu="">
>>> >>
>>> <mailto:sdmorris@u.washington.>>> <mailto:sdmorris@u.washington.**>____edu
>>> <mailto:sdmorris@u.washington.**__edu>>> <mailto:sdmorris@u.washington.**edu <sdmorris@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@u.washington.edu>>> <mailto:sdmorris@u.washington.**edu <sdmorris@u.washington.edu="">>
>>> <mailto:sdmorris@u.washington.**__edu>>> <mailto:sdmorris@u.washington.**edu <sdmorris@u.washington.edu="">
>>> >>
>>> <mailto:sdmorris@u.washington.>>> <mailto:sdmorris@u.washington.**>____edu
>>> <mailto:sdmorris@u.washington.**__edu>>> <mailto:sdmorris@u.washington.**edu <sdmorris@u.washington.edu="">
>>> >>>
>>> <mailto:sdmorris@u.washington>>> <mailto:sdmorris@u.washington>**.
>>> <mailto:sdmorris@u.washington>>> <mailto:sdmorris@u.washington>**.__>____edu
>>>
>>>
>>> <mailto:sdmorris@u.washington.>>> <mailto:sdmorris@u.washington.**>____edu
>>> <mailto:sdmorris@u.washington.**__edu>>> <mailto:sdmorris@u.washington.**edu <sdmorris@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@r-project.org
>>>
<mailto:bioconductor@r-**project.org<bioconductor@r-project.org>
>>> >
>>>
<mailto:bioconductor@r-__**project.org<bioconductor@r-__project.org>
>>>
<mailto:bioconductor@r-**project.org<bioconductor@r-project.org>
>>> >>
>>> <mailto:bioconductor@r-____**project.org<biocondu ctor@r-____project.org="">
>>>
<mailto:bioconductor@r-__**project.org<bioconductor@r-__project.org>
>>> >
>>>
<mailto:bioconductor@r-__**project.org<bioconductor@r-__project.org>
>>>
<mailto:bioconductor@r-**project.org<bioconductor@r-project.org>
>>> >>>
>>>
>>> <mailto:bioconductor@r-______**project.org<bioconductor@r- ______project.org="">
>>> <mailto:bioconductor@r-____**project.org<bioconductor@r-__ __project.org="">
>>> >
>>> <mailto:bioconductor@r-____**project.org<biocondu ctor@r-____project.org="">
>>>
<mailto:bioconductor@r-__**project.org<bioconductor@r-__project.org>
>>> >>
>>>
>>>
>>> <mailto:bioconductor@r-____**project .org<bioconductor@r-____project.org="">
>>>
<mailto:bioconductor@r-__**project.org<bioconductor@r-__project.org>
>>> >
>>>
<mailto:bioconductor@r-__**project.org<bioconductor@r-__project.org>
>>>
<mailto:bioconductor@r-**project.org<bioconductor@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
>>>
>>
>
>
> --
> -----
> *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@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@broadinstitute.org
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