Snptest (Gen/Sample) Files To R

Question

[Joey]

Does anyone know or can point me to any resource regarding how to convert SNPTEST dosage data files (GEN/SAMPLE) files so that they work in R/SAS? PLINK can read SNPTEST dosage format data but it seems that it can only perform association tests whereas I would like to perform a multinomial logistic regression.

Thanks,

-Joey

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EDIT: added the example data: I was given two sets of data: a) Hapmap2 imputed -> a series of files for each chromosome in standard SNPTEST format (GEN/SAMPLE) and a *.mlinfo file i.e. 66 files in total.

The *.mlinfo files looks like the following:

SNP POS A1 A2 REF_FREQ RSQ
rs10047182 4434181 A G 0.117476853526221 0.98222786900009
rs1009345 3576288 A G 0.395093490054250 0.389054499338887

b) 1000 genomes imputed dataset: IMPUTE v2 was used to get the files. For each chromosome, I have around 40-50 chunks depending on the # os SNPs in each.

I have a chunk1_info file which has the following:

np_id rs_id position exp_freq_a1 info certainty type info_type0 concord_type0 r2_type0
--- rs58108140 10583 0.125 0.025 0.765 0 -1 -1 -1
--- rs3877545 11508 1.000 0.000 1.000 0 -1 -1 -1

A infobysample file:

concord_type0 r2_type0
0.949 0.915
0.949 0.936

and the SNP information contained in each of the chunks:

--- rs4912140 20001071 T G 0 0 1 0 1 0 0 0 1 0 0 1 0 0 1 0 0 1 0 1 0 0 0 1 0 0 1 0 0 1 0.004 0.595 0.401 0 ........

I guess what I want is a file similar to the file one gets when one uses --recodeA option in PLINK. I can use the *.raw file along with covariates to run a bunch of other models (multinomial logit or cox prop, hazards model).

Thanks,

Joey

[Gaffa]

It could be helpful if you posted a small example of what this file format looks like, and perhaps also what you want to convert it to ("so that they work in R" is not very specific - R is pretty flexible and does not require strictly specified file formats).

[s.w.vanderlaan]

Just added a link to our GWASToolKit on GitHub: https://github.com/swvanderlaan/GWASToolKit.

Answer 1

[zx8754]

GenABEL package has a function impute2databel()

For analysis try ProbABEL.

This post might be helpful.

Answer 2

[s.w.vanderlaan]

Any interest for this issue? We made a bash- and a perl-script to convert impute2 data to (plink) style dosage data. If needed I can post a link to the scripts.

By popular demand. Here is the link to our beta-version of 'GWASToolKit': https://github.com/swvanderlaan/GWASToolKit. You can use one of the two files named 'convert_impute2dosage.pl' or 'convert_impute2dosage.sh' to convert impute2 data to dosages.

[Zaag]

Please do, if someone's future google adventure leads here they might order a hit on you if this is the last post.

[s.w.vanderlaan]

Just added a link to our GWASToolKit on GitHub: https://github.com/swvanderlaan/GWASToolKit.

[jlwebb]

I would be very interested in seeing your bash and perl scripts for this data conversion.

I had been looking into using Gtool for it but a simple bash script would be preferable in my eyes.

[s.w.vanderlaan]

Just added a link to our GWASToolKit on GitHub: https://github.com/swvanderlaan/GWASToolKit.

Answer 3

[Michael]

It seems like you can use read.table or scan as with any tabular text format. read ?read.table and ?scan. Use scan if read.table takes too long.