Fbm #23

dramanica · 2024-04-17T15:19:02Z

No description provided.

[skip ci]

Also remove the remove_ambiguous, as it was redundant

It needs a test!

we should create gen_tibbles without having to first create a bed file. Here we lay the foundations for that.

fullfils the basic requirements from #7

fix #9

This also changes the behaviour of loci_freq(), which becomes loci_alt_freq() to avoid any confusion Fixes #18

test gen_tibble error

Bring in adegenet and sNMF

this provides the basic functions for #16

we are only missing prediction, which is not that common a task.

Test loci ld

dramanica and others added 30 commits March 13, 2024 00:01

initial implementation with bigsnpr

4fc6d4b

bring back basic functionality

328d277

Fix all warnings.

e1028b4

bring back row_bind_dry_run

a34da10

rbind works again!

938ea1f

merging all working with explanation

d9f742b

bring back pca

7cc99dc

simplify vignettes

101b05d

simple imputation

72f8517

small typos

bbaf451

[skip ci]

clean up PCA implementation

07bc908

clean up interface to create gen_tibble

ade7c61

Also remove the remove_ambiguous, as it was redundant

add conversion from vcf to bed

7fa3d36

sort out tidiers for pca and add a standard PCA

0732d98

Imputation infrastructure

75d35bf

loci_missingness

b4585e3

add sums

f5131cf

It needs a test!

starting on fst

cb25fad

Bring back fst

d5c60bd

add randomised partial SVD

26cfba9

add rds file name to genotypes column

525d527

infrastructure to create gen_tibbles directly

a7d18de

we should create gen_tibbles without having to first create a bed file. Here we lay the foundations for that.

create gen_tibble from tables

63e0076

Add gt_write_plink

cc6e1a7

add loci_hwe

97909a4

simple implementation of loci_qc_report

43db89e

fullfils the basic requirements from #7

Faster hwe

6b95da0

alternative R implementation (similar speed)

d2c75c5

A basic vcf parser in the new fbm system.

411c5e8

load and save files

1ec2e11

fix #9

dramanica and others added 28 commits March 25, 2024 14:30

first untested version of ld clumping

a27f3e2

Change default number of pc for dapc

0a0f786

typo

183ed99

Implement loci_maf()

f8623d3

This also changes the behaviour of loci_freq(), which becomes loci_alt_freq() to avoid any confusion Fixes #18

Merge pull request #20 from EvolEcolGroup/test_matrix

c8b9fa8

test gen_tibble error

Bring in adegenet and sNMF

8006d88

fix ld_clump

53f3765

Merge branch 'fbm' of github.com:EvolEcolGroup/tidypopgen into fbm

5eccd7a

loci_ld_clump fix and basic test

0edcbea

Merge pull request #21 from EvolEcolGroup/snmf

d9a83bf

Bring in adegenet and sNMF

add autoplot for gt_pca

41d6e56

add tidiers for gt_dapc

7f0c22e

this provides the basic functions for #16

add autoplot for gt_pca_clust

fd8972b

small fixes

e96b0a1

fix dapc var loadings

f065029

Improve tidiers and autoplot

402a38d

better tidiers for pca

b5a56f8

dapc is now fully functional

5aec09c

we are only missing prediction, which is not that common a task.

typos

3545510

better handling of imputation

da01abf

Change n_cores to ncore to pass to bigsnpr SVD

c9d497c

Checking ncores = n_cores in SVD

24a3773

fix KING estimator

a6ea4ba

clean up ibs and king function

4a3250b

minor fixes on var names in c++

2500416

a few ibd notes

fd57647

fix KING

40b8134

Merge pull request #22 from EvolEcolGroup/test_loci_ld

9fa1fff

Test loci ld

dramanica merged commit f61edf3 into main Apr 17, 2024
1 check passed

dramanica deleted the fbm branch April 24, 2024 08:24

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Fbm #23

Fbm #23

dramanica commented Apr 17, 2024

Fbm #23

Fbm #23

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dramanica commented Apr 17, 2024