Open krostifangers opened 6 years ago
Is it possible to give the command you used for norm
and possibly even one of your output files for me to look at?
Hi thank you for your answer. I used the following command line ./norm --ihh12 --files ihh12Wild*.out --crit-percent 0.001 this kind of command worked for all other statistics (XP-EHH, IHS, nSL) and please find here a output file thank you in advance All the best christophe
De: "Zachary A Szpiech" notifications@github.com À: "szpiech/selscan" selscan@noreply.github.com Cc: "Christophe LEMAIRE" christophe.lemaire@univ-angers.fr, "Author" author@noreply.github.com Envoyé: Mardi 24 Avril 2018 15:27:35 Objet: Re: [szpiech/selscan] ihh12 normalization (#29)
Is it possible to give the command you used for norm and possibly even one of your output files for me to look at?
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Thanks. I'm not sure what happened to the file (I don't see it attached), but I will do some testing and look into this very soon.
I re-send the output file
De: "Zachary A Szpiech" notifications@github.com À: "szpiech/selscan" selscan@noreply.github.com Cc: "Christophe LEMAIRE" christophe.lemaire@univ-angers.fr, "Author" author@noreply.github.com Envoyé: Mardi 24 Avril 2018 15:40:04 Objet: Re: [szpiech/selscan] ihh12 normalization (#29)
Thanks. I'm not sure what happened to the file (I don't see it attached), but I will do some testing and look into this very soon.
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Sorry, would you email it to me directly at zachary.szpiech@ucsf.edu. I'm either badly missing something or github isn't letting it through.
I'm curious if this issue was ever resolved? I seem to be observing a slightly off Gaussian distribution in the ihh12 statistic after performing normalization. Please see image at bottom and code used to calculate and normalize ihh12. Thanks so much!
Code for selection scans:
selscan --ihh12 --pmap --threads ${sscnThreads} --vcf ${chrVcf} --map ${chrMap} --out ${chrIhh12}
Codes for normalization:
norm --ihh12 --files ${dir}chr1${fl} ${dir}chr2${fl} ${dir}chr3${fl} ${dir}chr4${fl} ${dir}chr5${fl} ${dir}chr6${fl} ${dir}chr7${fl} ${dir}chr8${fl} ${dir}chr9${fl} ${dir}chr10${fl} ${dir}chr11${fl} ${dir}chr12${fl} ${dir}chr13${fl} ${dir}chr14${fl} ${dir}chr15${fl} ${dir}chr16${fl} ${dir}chr17${fl} ${dir}chr18${fl} ${dir}chr19${fl} ${dir}chr20${fl} ${dir}chr21${fl} ${dir}chr22${fl}
Hi there, this may be due to the fact that raw ihh12 is theoretically bound in [0,1] (unlike iHS, et al which are in (-\infty,\infty), but I'm not too sure at the moment.
Hi all,
I would like to know the header information of the ihh12 norm window output, it has 5 columns such as: 1 50001 116 0.422414 100 I can tell the first three are window start, end, and SNP numbers. Then the last two are <frac of |iHS| > threshold>
Hello,
So the columns are,
Hi I tried to normalize ihh12 files but the distribution i finally obtained was not zero-centered and did not look like normal. So I do not know what's going on.Could you help me? Thank you in advance All the best christophe