User: Sam Rose

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Sam Rose60
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Posts by Sam Rose

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GWATools use in creating ncdf files
... Hi Stephanie, Quick question, do you have any experience with the following error in the ncdfAddData() function? Error in `[.data.frame`(dat, , new.names) : undefined columns selected > traceback() 4: stop("undefined columns selected") 3: `[.data.frame`(dat, , new.names) 2: dat[, new.names] 1: n ...
snp annotation cdf gwastools written 6.2 years ago by Sam Rose60 • updated 6.2 years ago by Stephanie M. Gogarten680
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Comment: C: GWATools use in creating ncdf files
... Hi Stephanie, After using your commands I was able to successfully use the package without error. I think the error was within the column names, which needed to be changed from genoRunID to scanID in order to be recognized by the later commands. Thanks for all of your help it was very much apprec ...
written 6.3 years ago by Sam Rose60
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Comment: C: GWATools use in creating ncdf files
... Hi Stephanie, I am providing a CEU control sample data from the same study, NA12878. I just sent it to you in a dropbox link. Let me know if there are any questions. Best, Sam On Wed, Jun 5, 2013 at 12:11 PM, Stephanie M. Gogarten < sdmorris@u.washington.edu> wrote: > It's not findin ...
written 6.3 years ago by Sam Rose60
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Answer: A: GWATools use in creating ncdf files
... Yes this was intentional. I just wanted to get it running for one sample and then expand to the rest. I was also limiting this to only autosomes for the time being. This is the error message I get now: > seg <- anomSegmentBAF(blData, genoData, scan.ids=scan.ids, + ...
written 6.3 years ago by Sam Rose60
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Answer: A: GWATools use in creating ncdf files
... Looks like there was some problems reading the file in on my end, some chromosomes didn't make it in probably from a preprocessing step on my end. I'll let you know if I can't rectify. Thanks again for the help, Sam On Thu, May 30, 2013 at 4:43 PM, Stephanie M. Gogarten < sdmorris@u.washingto ...
written 6.3 years ago by Sam Rose60
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Answer: A: GWATools use in creating ncdf files
... Thank you for your previous help Stephanie. I am afraid I have another problem I can't seem to work out. I have gotten as far as reading in the BAlleleFreq and Geno files into their respective ncdf formats. I only have the baf data in the intensity ncdf file, do I need LRR too? When I run the anom ...
written 6.3 years ago by Sam Rose60

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