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    Thread: Code for fst distances on qpadm
Post: Code for fst distances on qpadm

Hi can someone remind me what the code was for admixtools2 to do fst distances 
Genetics189291
Genetics189291
Inquiries Corner 1 177 06-21-2024, 05:03 PM
    Thread: sons admixtools2 run
Post: RE: sons admixtools2 run

Mulay 'Abdullah Wrote: (05-11-2024, 03:37 PM) -- Genetics189291 Wrote: (05-10-2024, 09:22 PM) -- Mozabite Code: -- > qp$weights # A tibble: 4 × 5   target      left                        weight  ...
Genetics189291
Genetics189291
Autosomal (auDNA) 6 257 05-11-2024, 04:43 PM
    Thread: sons admixtools2 run
Post: RE: sons admixtools2 run

Mozabite Code: -- > qp$weights # A tibble: 4 × 5   target      left                        weight      se    z                                   1 Mozabite.DG CanaryIslands_Guanche.SG    0.799 ...
Genetics189291
Genetics189291
Autosomal (auDNA) 6 257 05-10-2024, 09:22 PM
    Thread: sons admixtools2 run
Post: RE: sons admixtools2 run

Code: -- > qp$weights # A tibble: 3 × 5   target left                        weight    se    z                               1 Son    CanaryIslands_Guanche.SG    0.730 0.0484 15.1 2 Son   ...
Genetics189291
Genetics189291
Autosomal (auDNA) 6 257 05-10-2024, 08:55 PM
    Thread: North African QPADM runs
Post: RE: North African QPADM runs

abceff Wrote: (12-02-2023, 10:16 AM) -- Code: -- > results$weights # A tibble: 3 × 5   target left                weight     se     z                       1 abceff Mozabite.HO         0.639  ...
Genetics189291
Genetics189291
Northern 15 889 05-10-2024, 04:37 PM
    Thread: sons admixtools2 run
Post: RE: sons admixtools2 run

With papuan added Code: -- > qp$weights # A tibble: 3 × 5 target left weight se z 1 Son Mozabite.DG 0.902 0.0227 39.8 2 Son Yoruba.DG 0.0541 0.0149 3.62 3...
Genetics189291
Genetics189291
Autosomal (auDNA) 6 257 05-10-2024, 04:32 PM
    Thread: sons admixtools2 run
Post: RE: sons admixtools2 run

two way modelling for my son Code: -- > qp$weights # A tibble: 2 × 5   target left                        weight    se    z                               1 Son    CanaryIslands_Guanche.SG  ...
Genetics189291
Genetics189291
Autosomal (auDNA) 6 257 05-10-2024, 03:13 PM
    Thread: sons admixtools2 run
Post: sons admixtools2 run

Code: -- > > qp$weights # A tibble: 3 × 5 target left weight se z 1 Son CanaryIslands_Guanche.SG 0.711 0.0499 14.2 2 So...
Genetics189291
Genetics189291
Autosomal (auDNA) 6 257 05-10-2024, 11:48 AM
    Thread: Commands for admixtools2
Post: RE: Commands for admixtools2

Code: -- > results$weights # A tibble: 4 × 5 target left weight se z 1 Son Mozabite.DG 0.914 0.0674 13.6 2 Son BedouinB.DG -0.224 0.199 -1.12 3...
Genetics189291
Genetics189291
Inquiries Corner 2 141 05-10-2024, 10:01 AM
    Thread: Commands for admixtools2
Post: Commands for admixtools2

What’s the command to also show the p rate I forgot how to add it
Genetics189291
Genetics189291
Inquiries Corner 2 141 05-10-2024, 09:57 AM
    Thread: Right populations to use for qpadm
Post: RE: Right populations to use for qpadm

Kale Wrote: (05-08-2024, 08:06 PM) -- What time period are you looking at for sources/left pops? -- A mixture of moderns, Iron Age and medieval thanks
Genetics189291
Genetics189291
Inquiries Corner 3 186 05-08-2024, 08:19 PM
    Thread: Right populations to use for qpadm
Post: Right populations to use for qpadm

Does anyone have a list of good right populations to use for north west Africans, also I need samples that can differentiate Arab and Levantine ancestry thanks
Genetics189291
Genetics189291
Inquiries Corner 3 186 05-08-2024, 07:59 PM
    Thread: Datasets for North African samples
Post: RE: Datasets for North African samples

I’m looking for Berber samples etc shilha and Kabyle samples if possible
Genetics189291
Genetics189291
Inquiries Corner 2 97 05-08-2024, 02:54 PM
    Thread: Datasets for North African samples
Post: Datasets for North African samples

Can someone point me in the direction of datasets with more Berber samples so I can merge them with mine
Genetics189291
Genetics189291
Inquiries Corner 2 97 05-08-2024, 02:26 PM
    Thread: Dataset merging help
Post: RE: Dataset merging help

It’s okay I seemed to have a found a way to merge it directly which is much easier then converting it back and forth, takes a fraction of the time I’ll go through the steps when I get back home
Genetics189291
Genetics189291
Inquiries Corner 23 1,652 05-08-2024, 09:53 AM
    Thread: Dataset merging help
Post: RE: Dataset merging help

Anglesqueville Wrote: (05-07-2024, 02:20 PM) -- Genetics189291, I'm seemingly on your ignore list. I can't therefore reply to your PM. I guess you want to convert from PLINK to EIGENSTRAT? If this is...
Genetics189291
Genetics189291
Inquiries Corner 23 1,652 05-07-2024, 03:28 PM
    Thread: Dataset merging help
Post: RE: Dataset merging help

AimSmall Wrote: (05-05-2024, 11:34 PM) -- Post the head of the file -- Don’t know what I’m doing wrong but when I’m converting the file back after merging it, it just has control next to the ids
Genetics189291
Genetics189291
Inquiries Corner 23 1,652 05-06-2024, 08:45 PM
    Thread: Dataset merging help
Post: RE: Dataset merging help

AimSmall Wrote: (05-05-2024, 11:34 PM) -- Post the head of the file -- I’ve seemed to fix that issue but not my problem is when I’m converting the file back after merging the names are not showing ...
Genetics189291
Genetics189291
Inquiries Corner 23 1,652 05-06-2024, 06:17 AM
    Thread: Dataset merging help
Post: RE: Dataset merging help

AimSmall Wrote: (05-05-2024, 06:38 PM) -- plink --23file 23andme_raw_data.txt --make-bed --out mydata -- I got to the bit of merging the two files but I’m getting this now  Error: Line 1 of v54....
Genetics189291
Genetics189291
Inquiries Corner 23 1,652 05-05-2024, 10:34 PM
    Thread: Dataset merging help
Post: RE: Dataset merging help

AimSmall Wrote: (05-05-2024, 06:38 PM) -- plink --23file 23andme_raw_data.txt --make-bed --out mydata -- That seemed to work , if I remember what you taught me i have to convert the dataset into the...
Genetics189291
Genetics189291
Inquiries Corner 23 1,652 05-05-2024, 06:56 PM