Index

Symbols

--adj-pval genrisk-find-association command line option --af-col genrisk-score-genes command line option --alt-col genrisk-score-genes command line option --annotation-file genrisk-score-genes command line option --beta-param genrisk-score-genes command line option --bfiles genrisk-score-genes command line option --chr-col genrisk-visualize command line option --covariates genrisk-find-association command line option --data-file genrisk-create-model command line option genrisk-normalize command line option --del-col genrisk-score-genes command line option --feature-selection genrisk-create-model command line option --folds genrisk-create-model command line option --gene-col genrisk-score-genes command line option --genes genrisk-find-association command line option --genes-col genrisk-normalize command line option --genes-info genrisk-normalize command line option --genescol-1 genrisk-visualize command line option --genescol-2 genrisk-visualize command line option --imbalanced genrisk-create-model command line option --include-models genrisk-create-model command line option --info-file genrisk-find-association command line option genrisk-visualize command line option --input-file genrisk-test-model command line option --keep genrisk-score-genes command line option --label-col genrisk-test-model command line option --lengths-col genrisk-normalize command line option --maf-threshold genrisk-score-genes command line option --method genrisk-normalize command line option --metric genrisk-create-model command line option --model-name genrisk-create-model command line option --model-path genrisk-test-model command line option --model-type genrisk-create-model command line option genrisk-test-model command line option --normalize genrisk-create-model command line option --normalize-method genrisk-create-model command line option --output-file genrisk-normalize command line option genrisk-score-genes command line option genrisk-test-model command line option --output-folder genrisk-create-model command line option --phenotype genrisk-find-association command line option --plink genrisk-get-prs command line option genrisk-score-genes command line option --pos-col genrisk-visualize command line option --processes genrisk-find-association command line option --pval-col genrisk-visualize command line option

--pvals-file genrisk-visualize command line option --samples-col genrisk-create-model command line option genrisk-find-association command line option genrisk-normalize command line option genrisk-test-model command line option --scores-file genrisk-find-association command line option --seed genrisk-create-model command line option --target-col genrisk-create-model command line option --temp-dir genrisk-score-genes command line option --test genrisk-find-association command line option --test-size genrisk-create-model command line option --variant-col genrisk-score-genes command line option --weight-func genrisk-score-genes command line option --zero-threshold genrisk-find-association command line option -a genrisk-find-association command line option genrisk-score-genes command line option -b genrisk-create-model command line option genrisk-score-genes command line option -c genrisk-find-association command line option genrisk-visualize command line option -d genrisk-create-model command line option genrisk-score-genes command line option -f genrisk-create-model command line option genrisk-score-genes command line option -g genrisk-find-association command line option genrisk-score-genes command line option -i genrisk-create-model command line option genrisk-find-association command line option genrisk-test-model command line option genrisk-visualize command line option -k genrisk-score-genes command line option -l genrisk-create-model command line option genrisk-score-genes command line option genrisk-test-model command line option -m genrisk-create-model command line option genrisk-find-association command line option genrisk-normalize command line option genrisk-score-genes command line option genrisk-test-model command line option -n genrisk-create-model command line option -o genrisk-create-model command line option genrisk-normalize command line option genrisk-score-genes command line option genrisk-test-model command line option -p genrisk-find-association command line option genrisk-get-prs command line option genrisk-score-genes command line option genrisk-visualize command line option -s genrisk-find-association command line option genrisk-test-model command line option genrisk-visualize command line option -t genrisk-find-association command line option genrisk-score-genes command line option genrisk-test-model command line option -v genrisk-find-association command line option genrisk-score-genes command line option genrisk-visualize command line option -w genrisk-score-genes command line option

B

betareg_pvalues() (in module genrisk.pipeline)

C

create_prediction_model() (in module genrisk.pipeline)

D

draw_manhattan() (in module genrisk.utils)

draw_qqplot() (in module genrisk.utils)

F

find_pvalue() (in module genrisk.pipeline)

G

genrisk-create-model command line option --data-file --feature-selection --folds --imbalanced --include-models --metric --model-name --model-type --normalize --normalize-method --output-folder --samples-col --seed --target-col --test-size -b -d -f -i -l -m -n -o genrisk-find-association command line option --adj-pval --covariates --genes --info-file --phenotype --processes --samples-col --scores-file --test --zero-threshold -a -c -g -i -m -p -s -t -v genrisk-get-prs command line option --plink -p genrisk-normalize command line option --data-file --genes-col --genes-info --lengths-col --method --output-file --samples-col -m -o

genrisk-score-genes command line option --af-col --alt-col --annotation-file --beta-param --bfiles --del-col --gene-col --keep --maf-threshold --output-file --plink --temp-dir --variant-col --weight-func -a -b -d -f -g -k -l -m -o -p -t -v -w genrisk-test-model command line option --input-file --label-col --model-path --model-type --output-file --samples-col -i -l -m -o -s -t genrisk-visualize command line option --chr-col --genescol-1 --genescol-2 --info-file --pos-col --pval-col --pvals-file -c -i -p -s -v

N

normalize_data() (in module genrisk.pipeline)

S

scoring_process() (in module genrisk.pipeline)