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descriptives.scan how to save output

Posted: Thu Jun 23, 2016 10:09 am
by kapr_genabel
Hello GenABEL users.



I am doing GWAS of a fungal genome that has more than One Million SNPs.

This is my first time analysis with GenABEL. I would like to know how to save the descriptives.scan results into a file. (i was able to save top 10, 100 etc,)
but I wanted to save all the hits into a file.

below is the commands i tried to save the output which dint work.

Code: Select all

descanmaf03 <- descriptives.scan(qtmaf03)
dscanresults <- descanmaf03@results
 write.table(dscanresults,file="~/path to/descanmaf03.txt",sep="\t")


also in tired sink()

Code: Select all

sink(file='descanmaf03.txt')
descriptives.scan(qtmaf03)
sink()


both the above scripts gives me an error or only saves top 1o results.
"sorry if the question looks silly, but i trying to learn"

Thank you
KRP

Re: descriptives.scan how to save output

Posted: Thu Jun 23, 2016 5:05 pm
by lckarssen
What do you plan to do with the saved data? Is it acceptable if the file is only readable from R? Or should it be, for example, a text file (e.g. a .csv file)?

Re: descriptives.scan how to save output

Posted: Wed Jul 06, 2016 1:23 pm
by kapr_genabel
Hi sorry for the delayed reply.
I wanted it in a text file. anyways i have figured it out thank you for your response.

KRP