problem with impute2databel() function

Questions about GenABEL (aka *ABEL) suite of packages
Forum rules
Please remember not to post any sensitive data on this public forum.
The first few posts of newly registered users will be moderated in order to filter out any spammers.

When get a solution to the problem you posted, please change the topic name (e.g. from "how to ..." to "[SOLVED] how to ..."). This will make it easier for the community to follow the posts yet to be attended.
Kevin_Lu
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

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

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
PolyOmica
The Netherlands
-------


Return to “GenABEL”

Who is online

Users browsing this forum: Bing [Bot] and 1 guest