Question: how to interpret LOSITAN output?
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gravatar for ralbreiki7
2.8 years ago by
ralbreiki70
ralbreiki70 wrote:

Hi everyone,

I have a SNPs dataset of approx 9000 Loci, 225 individuals assembling 4 distant populations. Currently I am interested in identifying outliers therefore, I run LOSITAN. I think the output doesn't make much sense to me. As further as I know the software l highlights potential directional loci in red, balancing in yellow, neutral in wight. I kept the confidence interval as default 0.95.

It gave me red rows tagged with outlier in the section of FDR, but all with a high p(simulated fst<sample fst)="" is="" equals="" or="" greater="" than="" 96.="" as="" far="" as="" i="" understood="" the="" p(simulated="" fst<sample="" fst)="" is="" just="" the="" same="" as="" the="" usual="" p-value.="" in="" this="" sense="" i="" have="" no="" directional="" loci="" in="" this="" data="" even="" between="" two="" distant="" pops="" like="" vietnam="" and="" oman,="" while="" i="" got="" some="" with="" bayescan!<="" p="">

Can any one help me with this.

Best,

R

snp • 1.0k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by ralbreiki70
0
gravatar for ralbreiki7
2.8 years ago by
ralbreiki70
ralbreiki70 wrote:

Hi everyone,

I have a SNPs dataset of approx 9000 Loci, 225 individuals assembling 4 distant populations. Currently I am interested in identifying outliers therefore, I run LOSITAN. I think the output doesn't make much sense to me. As further as I know the software l highlights potential directional loci in red, balancing in yellow, neutral in wight. I kept the confidence interval as default 0.95.

It gave me red rows tagged with outlier in the section of FDR, but all with a high p(simulated fst<sample fst)="" is="" equals="" to="" or="" greater="" than="" 0.96.<="" p="">

As far as I understood the p(simulated fst< sample fst) is just the p-value.

In this sense, I don't have any directional loci in this data even between two distant pops like Vietnam and Oman!

While I got some with BayeScan!

Can anyone help me with this?

Best,

R

ADD COMMENTlink written 2.8 years ago by ralbreiki70
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