the function of impute2databel

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Kevin_Lu
Posts: 2
Joined: Thu Nov 07, 2013 6:58 pm

the function of impute2databel

Postby Kevin_Lu » Fri Nov 08, 2013 6:01 pm

Thanks for help. I still have problems in impute2 file to fvd and fvi files:

Code: Select all

> library (MASS)
> library(GenABEL)
GenABEL v. 1.7-6 (May 16, 2013) loaded

> library (DatABEL)
DatABEL v.0.9-4 (March 12, 2013) loaded

> impute2databel(genofile="/gs01/projects/ipm/data/imputation/final/combo_exome_wMonomorphic-chr1_imputed.0-5Mb.gen", samplefile="/hpc/users/luy05/Data_scripts/FM_CAD/Interaction/ipm-combo-preImpute_chr1.sample", outfile="/gs01/projects/ipm/data/kevin_imputation_results/CAD_Interaction/combo_exome_wMonomorphic_chr1_imputed_0_5Mb", makeprob=TRUE, old=FALSE)
Options in effect:
    --infile    = /gs01/projects/ipm/data/imputation/final/combo_exome_wMonomorphic-chr1_imputed.0-5Mb.gen
    --outfile   = ./tmp903142
    --skiprows  = OFF
    --skipcols  = 5
    --cnrow     = OFF
    --rncol     = ON, using column 2 of '/gs01/projects/ipm/data/imputation/final/combo_exome_wMonomorphic-chr1_imputed.0-5Mb.gen'
    --transpose = ON
    --Rmatrix   = OFF
    --nanString = NA
Number of lines in source file is 65708
Number of words in source file is 41135
skiprows = 0
cnrow = 0
skipcols = 5
rncol = 2
Rmatrix = 0
numWords = 41135
Creating file with numRows = 65708
Creating file with numColumns = 41130
text2fvf finished.
Error in .Call("iterator", tmp_fv@data, as.integer(0), as.integer(0),  :
  "iterator" not resolved from current namespace (GenABEL)
Calls: impute2databel -> .Call
Execution halted

kyriaki
Posts: 4
Joined: Fri Nov 22, 2013 10:03 am

Re: the function of impute2databel

Postby kyriaki » Fri Nov 22, 2013 10:30 am

I have the same issue with impute2databel :
For the same data, with an out of date GenABEL and DatABEL it works fine :

Code: Select all

library(GenABEL)
Loading required package: MASS
GenABEL v. 1.6-9 (August 30, 2011) loaded

Installed GenABEL version (1.6-9) is not the same as stable
version available from CRAN (1.7-0). Unless used intentionally,
consider updating to the latest CRAN version. For that, use
'install.packages("GenABEL")', or ask your system administrator
to update the package.

> library(DatABEL)
DatABEL v. 0.9-2 (October 17, 2010) loaded
> impute2databel("tmp1","chr2.sample","tmp1_out")
Options in effect:
    --infile    = tmp1
    --outfile   = ./tmp944797
    --skiprows  = OFF
    --skipcols  = 5
    --cnrow     = OFF
    --rncol     = ON, using column 2 of 'tmp1'
    --transpose = ON
    --Rmatrix   = OFF
    --nanString = NA
Number of lines in source file is 5
Number of words in source file is 8591
skiprows = 0
cnrow = 0
skipcols = 5
rncol = 2
Rmatrix = 0
numWords = 8591
Creating file with numRows = 5
Creating file with numColumns = 8586
text2fvf finished.
Loss of precision / loss of data during conversion from DOUBLE to FLOAT.
Futher conversion warnings omitted.
Read 11 items
Read 11 items
Read 11 items
Read 31482 items
uninames$unique.names = TRUE
uninames$unique.rownames = TRUE
uninames$unique.colnames = TRUE
backingfilename = tmp1_out.dose
cachesizeMb = 64
number of columns (variables) =  5
number of rows (observations) =  2862
usedRowIndex: 1  2  3  4  5  ...
usedColIndex: 1  2  3  4  5 
Upper-left 5 columns and  5 rows:
       rs183605628 rs34920961 rs1179724 rs34233293 rs1179723
1           0      0.000     2.000      0.000         2
2           0      0.000     0.000      0.000         0
3           0      0.000     2.000      0.000         2
6           0      0.984     1.000      0.991         1
7           0      0.001     1.008      0.000         1


With the latest version

Code: Select all

> library(GenABEL)
Loading required package: MASS
GenABEL v. 1.7-6 (May 16, 2013) loaded

> library(DatABEL)
DatABEL v.0.9-4 (March 12, 2013) loaded

impute2databel("tmp1","chr2.sample","tmp1_out")
Options in effect:
    --infile    = tmp1
    --outfile   = ./tmp195580
    --skiprows  = OFF
    --skipcols  = 5
    --cnrow     = OFF
    --rncol     = ON, using column 2 of 'tmp1'
    --transpose = ON
    --Rmatrix   = OFF
    --nanString = NA
Number of lines in source file is 5
Number of words in source file is 8591
skiprows = 0
cnrow = 0
skipcols = 5
rncol = 2
Rmatrix = 0
numWords = 8591
Creating file with numRows = 5
Creating file with numColumns = 8586
text2fvf finished.
Error in .Call("iterator", tmp_fv@data, as.integer(0), as.integer(0),  :
  "iterator" not resolved from current namespace (GenABEL)
Last edited by lckarssen on Mon Nov 25, 2013 10:04 am, edited 1 time in total.
Reason: Reformatted output with the [code] tag

lckarssen
Site Admin
Site Admin
Posts: 322
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: the function of impute2databel

Postby lckarssen » Mon Nov 25, 2013 10:04 am

Thanks for the update on this issue. This is helpful in determining the location of the bug! In fact, we are working on a solution and I expect it to land in the next release of GenABEL.
-------
Lennart Karssen
PolyOmica
The Netherlands
-------

Nasim
Posts: 1
Joined: Tue Dec 17, 2013 11:43 am

Re: the function of impute2databel

Postby Nasim » Tue Dec 17, 2013 11:47 am

Do you have any anticipated date for the next release? I also need to use impute2databel and am getting the same error message. Thank you very much.

lckarssen
Site Admin
Site Admin
Posts: 322
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: the function of impute2databel

Postby lckarssen » Fri Dec 20, 2013 8:57 am

At the moment we are working on uploading the new release to CRAN. However, recently the requirements for CRAN uploads have become much more stringent, so we are in the process of ironing out these extra checks.
Hopefully we have everything ready after New Year.
-------
Lennart Karssen
PolyOmica
The Netherlands
-------


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