problem with impute2databel() function

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

Re: problem with impute2databel() function

Postby Kevin_Lu » Thu Nov 07, 2013 7:18 pm

Dear all, I am trying to convert the impute2 data to fvd and fvi format. I encountered a mistake. Thanks for your help. Could something be wrong during the installation of GenABEL?

Code: Select all

> library (MASS)
> library(GenABEL)
connect: Network is unreachable
connect: Network is unreachable
connect: Network is unreachable
GenABEL v. 1.7-6 (May 16, 2013) loaded

> library (DatABEL)
connect: Network is unreachable
connect: Network is unreachable
connect: Network is unreachable
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   = ./tmp441133
    --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
Last edited by lckarssen on Sun Nov 10, 2013 8:20 pm, edited 1 time in total.
Reason: Reformatted output with the [code] tag

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Re: problem with impute2databel() function

Postby lckarssen » Tue Jan 28, 2014 4:18 pm

This issue should be resolved in GenABEL v1.8-0. If not, please let us know!
Lennart Karssen
The Netherlands

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