bsmith89 / micro.glmm

Purpose to Make an deploy Micro.glmm R package and files to run it

Instructions on how to run

Install Conda

conda env create -f microglmm.yml
conda activate microglmm

install package

From R

R
library(devtools)
install_github('miriam-goldman/micro.glmm')

run prep snps

Rscript src/prep_snps_command_line.R  --species_id exp_species -v TRUE  -o "example_output"
-i "example_data/exp_species.snps_info.tsv"
-f "example_data/exp_species.snps_freqs.tsv"
-d "example_data/exp_species.snps_depth.tsv"
-a 3 -m 5  -n 5   

For easier copy

Rscript src/prep_snps_command_line.R  --species_id exp_species -v TRUE  -o "example_output" -i "example_data/exp_species.snps_info.tsv" -f "example_data/exp_species.snps_freqs.tsv" -d "example_data/exp_species.snps_depth.tsv" -a 3 -m 5  -n 5   

run prep genes

Rscript src/prep_genes_command_line.R --species_id exp_species -v TRUE -o "example_output"
-c "example_data/exp_species.genes_copynum.tsv"
-d "example_data/exp_species.genes_depth.tsv"
-m 5 -n 5 --GRM example_output/exp_species.GRM.tsv --write_csv TRUE

For easier copy

Rscript src/prep_genes_command_line.R --species_id exp_species -v TRUE -o "example_output" -c "example_data/exp_species.genes_copynum.tsv" -d "example_data/exp_species.genes_depth.tsv" -m 5 -n 5 --GRM example_output/exp_species.GRM.tsv --write_csv TRUE

run population structure test

Rscript src/pop_structure_test_command_line.R --species_id exp_species -v TRUE -o example_output
--GRM example_output/exp_species.GRM.tsv
--metadata example_data/exp_metadata.tsv
--tau 1 --n_tau 10

For easier copy

Rscript src/pop_structure_test_command_line.R --species_id exp_species -v TRUE -o example_output --GRM example_output/exp_species.GRM.tsv --metadata example_data/exp_metadata.tsv --tau 1 --n_tau 10

Run Maker test

Rscript src/marker_test_command_line.R --species_id exp_species -v TRUE
-o example_output
--Rdata example_output/exp_species.model_obj.Rdata
--copy_number example_output/exp_species.copynumber_data.csv

For easier copy

Rscript src/marker_test_command_line.R --species_id exp_species -v TRUE -o example_output --Rdata example_output/exp_species.model_obj.Rdata --copy_number example_output/exp_species.copynumber_data.csv