Index

Symbols

--bonferroni clarite-cli-analyze-get-significant command line option --bonferroni <bonferroni> clarite-cli-plot-manhattan command line option --cat_max <cat_max> clarite-cli-modify-categorize command line option --cat_min <cat_min> clarite-cli-modify-categorize command line option --categories <categories> clarite-cli-plot-manhattan command line option clarite-cli-plot-manhattan-bonferroni command line option clarite-cli-plot-manhattan-fdr command line option --cluster <cluster> clarite-cli-analyze-ewas command line option clarite-cli-analyze-ewas-r command line option --comparison <comparison> clarite-cli-modify-rowfilter command line option --cont_min <cont_min> clarite-cli-modify-categorize command line option --covariance-calc <covariance_calc> clarite-cli-analyze-ewas command line option clarite-cli-analyze-ewas-r command line option --covariate <covariate> clarite-cli-analyze-ewas command line option clarite-cli-analyze-ewas-r command line option --current-float <cf> clarite-cli-modify-recode-values command line option --current-int <ci> clarite-cli-modify-recode-values command line option --current-str <cs> clarite-cli-modify-recode-values command line option --cutoff <cutoff> clarite-cli-modify-remove-outliers command line option clarite-cli-plot-manhattan-bonferroni command line option clarite-cli-plot-manhattan-fdr command line option --dropna clarite-cli-describe-skewness command line option --fdr clarite-cli-analyze-get-significant command line option --fdr <fdr> clarite-cli-plot-manhattan command line option clarite-cli-plot-manhattan-bonferroni command line option clarite-cli-plot-manhattan-fdr command line option --filter-percent <filter_percent> clarite-cli-modify-colfilter-percent-zero command line option --fpc <fpc> clarite-cli-analyze-ewas command line option clarite-cli-analyze-ewas-r command line option --how <how> clarite-cli-modify-merge-variables command line option --index <index> clarite-cli-load-from-csv command line option clarite-cli-load-from-tsv command line option --keepna clarite-cli-describe-skewness command line option --kind <kind> clarite-cli-plot-distributions command line option --label <label> clarite-cli-plot-manhattan command line option clarite-cli-plot-manhattan-bonferroni command line option clarite-cli-plot-manhattan-fdr command line option --method <method> clarite-cli-modify-remove-outliers command line option --min-n <min_n> clarite-cli-analyze-ewas command line option clarite-cli-analyze-ewas-r command line option --ncols <ncols> clarite-cli-plot-distributions command line option --nested clarite-cli-analyze-ewas command line option clarite-cli-analyze-ewas-r command line option --nlabeled <nlabeled> clarite-cli-plot-manhattan command line option clarite-cli-plot-manhattan-bonferroni command line option clarite-cli-plot-manhattan-fdr command line option --no-sort clarite-cli-plot-distributions command line option --not-nested clarite-cli-analyze-ewas command line option clarite-cli-analyze-ewas-r command line option --nrows <nrows> clarite-cli-plot-distributions command line option --only <only> clarite-cli-load-from-csv command line option clarite-cli-load-from-tsv command line option clarite-cli-modify-colfilter command line option clarite-cli-modify-colfilter-min-cat-n command line option clarite-cli-modify-colfilter-min-n command line option clarite-cli-modify-colfilter-percent-zero command line option clarite-cli-modify-drop-extra-categories command line option clarite-cli-modify-make-binary command line option clarite-cli-modify-make-categorical command line option clarite-cli-modify-make-continuous command line option clarite-cli-modify-move-variables command line option clarite-cli-modify-recode-values command line option clarite-cli-modify-remove-outliers command line option clarite-cli-modify-rowfilter-incomplete-obs command line option clarite-cli-modify-transform-variable command line option --other <other> clarite-cli-plot-manhattan command line option clarite-cli-plot-manhattan-bonferroni command line option clarite-cli-plot-manhattan-fdr command line option --output_left <output_left> clarite-cli-modify-move-variables command line option --output_right <output_right> clarite-cli-modify-move-variables command line option --pvalue <pvalue> clarite-cli-analyze-get-significant command line option --quality <quality> clarite-cli-plot-distributions command line option --replacement-float <rf> clarite-cli-modify-recode-values command line option

--replacement-int <ri> clarite-cli-modify-recode-values command line option --replacement-str <rs> clarite-cli-modify-recode-values command line option --single-cluster <single_cluster> clarite-cli-analyze-ewas command line option clarite-cli-analyze-ewas-r command line option --skip <skip> clarite-cli-load-from-csv command line option clarite-cli-load-from-tsv command line option clarite-cli-modify-colfilter command line option clarite-cli-modify-colfilter-min-cat-n command line option clarite-cli-modify-colfilter-min-n command line option clarite-cli-modify-colfilter-percent-zero command line option clarite-cli-modify-drop-extra-categories command line option clarite-cli-modify-make-binary command line option clarite-cli-modify-make-categorical command line option clarite-cli-modify-make-continuous command line option clarite-cli-modify-move-variables command line option clarite-cli-modify-recode-values command line option clarite-cli-modify-remove-outliers command line option clarite-cli-modify-rowfilter-incomplete-obs command line option clarite-cli-modify-transform-variable command line option --sort clarite-cli-plot-distributions command line option --strata <strata> clarite-cli-analyze-ewas command line option clarite-cli-analyze-ewas-r command line option --survey-data <survey_data> clarite-cli-analyze-ewas command line option clarite-cli-analyze-ewas-r command line option --threshold <threshold> clarite-cli-describe-correlations command line option --value-float <vf> clarite-cli-modify-rowfilter command line option --value-int <vi> clarite-cli-modify-rowfilter command line option --value-str <vs> clarite-cli-modify-rowfilter command line option --weight <weight> clarite-cli-analyze-ewas command line option clarite-cli-analyze-ewas-r command line option --weights-file <weights_file> clarite-cli-analyze-ewas command line option clarite-cli-analyze-ewas-r command line option -c clarite-cli-analyze-ewas command line option clarite-cli-analyze-ewas-r command line option clarite-cli-modify-remove-outliers command line option clarite-cli-modify-rowfilter command line option clarite-cli-plot-manhattan command line option clarite-cli-plot-manhattan-bonferroni command line option clarite-cli-plot-manhattan-fdr command line option -h clarite-cli-modify-merge-variables command line option -i clarite-cli-load-from-csv command line option clarite-cli-load-from-tsv command line option -k clarite-cli-plot-distributions command line option -m clarite-cli-modify-remove-outliers command line option -n <n> clarite-cli-modify-colfilter-min-cat-n command line option clarite-cli-modify-colfilter-min-n command line option -o clarite-cli-load-from-csv command line option clarite-cli-load-from-tsv command line option clarite-cli-modify-colfilter command line option clarite-cli-modify-colfilter-min-cat-n command line option clarite-cli-modify-colfilter-min-n command line option clarite-cli-modify-colfilter-percent-zero command line option clarite-cli-modify-drop-extra-categories command line option clarite-cli-modify-make-binary command line option clarite-cli-modify-make-categorical command line option clarite-cli-modify-make-continuous command line option clarite-cli-modify-move-variables command line option clarite-cli-modify-recode-values command line option clarite-cli-modify-remove-outliers command line option clarite-cli-modify-rowfilter-incomplete-obs command line option clarite-cli-modify-transform-variable command line option clarite-cli-plot-manhattan command line option clarite-cli-plot-manhattan-bonferroni command line option clarite-cli-plot-manhattan-fdr command line option -p clarite-cli-analyze-get-significant command line option clarite-cli-modify-colfilter-percent-zero command line option -q clarite-cli-plot-distributions command line option -s clarite-cli-load-from-csv command line option clarite-cli-load-from-tsv command line option clarite-cli-modify-colfilter command line option clarite-cli-modify-colfilter-min-cat-n command line option clarite-cli-modify-colfilter-min-n command line option clarite-cli-modify-colfilter-percent-zero command line option clarite-cli-modify-drop-extra-categories command line option clarite-cli-modify-make-binary command line option clarite-cli-modify-make-categorical command line option clarite-cli-modify-make-continuous command line option clarite-cli-modify-move-variables command line option clarite-cli-modify-recode-values command line option clarite-cli-modify-remove-outliers command line option clarite-cli-modify-rowfilter-incomplete-obs command line option clarite-cli-modify-transform-variable command line option -t clarite-cli-describe-correlations command line option -w clarite-cli-analyze-ewas command line option clarite-cli-analyze-ewas-r command line option

B

BOTTOM clarite-cli-modify-merge-observations command line option

C

clarite-cli-analyze-add-corrected-pvals command line option EWAS_RESULT OUTPUT clarite-cli-analyze-ewas command line option --cluster <cluster> --covariance-calc <covariance_calc> --covariate <covariate> --fpc <fpc> --min-n <min_n> --nested --not-nested --single-cluster <single_cluster> --strata <strata> --survey-data <survey_data> --weight <weight> --weights-file <weights_file> -c -w DATA OUTCOME OUTPUT clarite-cli-analyze-ewas-r command line option --cluster <cluster> --covariance-calc <covariance_calc> --covariate <covariate> --fpc <fpc> --min-n <min_n> --nested --not-nested --single-cluster <single_cluster> --strata <strata> --survey-data <survey_data> --weight <weight> --weights-file <weights_file> -c -w DATA OUTCOME OUTPUT clarite-cli-analyze-get-significant command line option --bonferroni --fdr --pvalue <pvalue> -p EWAS_RESULT OUTPUT clarite-cli-describe-correlations command line option --threshold <threshold> -t DATA OUTPUT clarite-cli-describe-freq-table command line option DATA OUTPUT clarite-cli-describe-get-types command line option DATA OUTPUT clarite-cli-describe-percent-na command line option DATA OUTPUT clarite-cli-describe-skewness command line option --dropna --keepna DATA OUTPUT clarite-cli-load-from-csv command line option --index <index> --only <only> --skip <skip> -i -o -s INPUT OUTPUT clarite-cli-load-from-tsv command line option --index <index> --only <only> --skip <skip> -i -o -s INPUT OUTPUT clarite-cli-modify-categorize command line option --cat_max <cat_max> --cat_min <cat_min> --cont_min <cont_min> DATA OUTPUT clarite-cli-modify-colfilter command line option --only <only> --skip <skip> -o -s DATA OUTPUT clarite-cli-modify-colfilter-min-cat-n command line option --only <only> --skip <skip> -n <n> -o -s DATA OUTPUT clarite-cli-modify-colfilter-min-n command line option --only <only> --skip <skip> -n <n> -o -s DATA OUTPUT clarite-cli-modify-colfilter-percent-zero command line option --filter-percent <filter_percent> --only <only> --skip <skip> -o -p -s DATA OUTPUT clarite-cli-modify-drop-extra-categories command line option --only <only> --skip <skip> -o -s DATA OUTPUT clarite-cli-modify-make-binary command line option --only <only> --skip <skip> -o -s DATA OUTPUT clarite-cli-modify-make-categorical command line option --only <only> --skip <skip> -o -s DATA OUTPUT

clarite-cli-modify-make-continuous command line option --only <only> --skip <skip> -o -s DATA OUTPUT clarite-cli-modify-merge-observations command line option BOTTOM OUTPUT TOP clarite-cli-modify-merge-variables command line option --how <how> -h LEFT OUTPUT RIGHT clarite-cli-modify-move-variables command line option --only <only> --output_left <output_left> --output_right <output_right> --skip <skip> -o -s LEFT RIGHT clarite-cli-modify-recode-values command line option --current-float <cf> --current-int <ci> --current-str <cs> --only <only> --replacement-float <rf> --replacement-int <ri> --replacement-str <rs> --skip <skip> -o -s DATA OUTPUT clarite-cli-modify-remove-outliers command line option --cutoff <cutoff> --method <method> --only <only> --skip <skip> -c -m -o -s DATA OUTPUT clarite-cli-modify-rowfilter command line option --comparison <comparison> --value-float <vf> --value-int <vi> --value-str <vs> -c COLUMN DATA OUTPUT clarite-cli-modify-rowfilter-incomplete-obs command line option --only <only> --skip <skip> -o -s DATA OUTPUT clarite-cli-modify-transform-variable command line option --only <only> --skip <skip> -o -s DATA OUTPUT TRANSFORM_METHOD clarite-cli-plot-distributions command line option --kind <kind> --ncols <ncols> --no-sort --nrows <nrows> --quality <quality> --sort -k -q DATA OUTPUT clarite-cli-plot-histogram command line option DATA OUTPUT VARIABLE clarite-cli-plot-manhattan command line option --bonferroni <bonferroni> --categories <categories> --fdr <fdr> --label <label> --nlabeled <nlabeled> --other <other> -c -o EWAS_RESULT OUTPUT clarite-cli-plot-manhattan-bonferroni command line option --categories <categories> --cutoff <cutoff> --fdr <fdr> --label <label> --nlabeled <nlabeled> --other <other> -c -o EWAS_RESULT OUTPUT clarite-cli-plot-manhattan-fdr command line option --categories <categories> --cutoff <cutoff> --fdr <fdr> --label <label> --nlabeled <nlabeled> --other <other> -c -o EWAS_RESULT OUTPUT clarite.analyze module clarite.analyze.regression module clarite.describe module clarite.load module clarite.modify module clarite.plot module clarite.survey module COLUMN clarite-cli-modify-rowfilter command line option

D

DATA clarite-cli-analyze-ewas command line option clarite-cli-analyze-ewas-r command line option clarite-cli-describe-correlations command line option clarite-cli-describe-freq-table command line option clarite-cli-describe-get-types command line option clarite-cli-describe-percent-na command line option clarite-cli-describe-skewness command line option clarite-cli-modify-categorize command line option clarite-cli-modify-colfilter command line option clarite-cli-modify-colfilter-min-cat-n command line option clarite-cli-modify-colfilter-min-n command line option clarite-cli-modify-colfilter-percent-zero command line option clarite-cli-modify-drop-extra-categories command line option clarite-cli-modify-make-binary command line option clarite-cli-modify-make-categorical command line option clarite-cli-modify-make-continuous command line option clarite-cli-modify-recode-values command line option clarite-cli-modify-remove-outliers command line option clarite-cli-modify-rowfilter command line option clarite-cli-modify-rowfilter-incomplete-obs command line option clarite-cli-modify-transform-variable command line option clarite-cli-plot-distributions command line option clarite-cli-plot-histogram command line option

E

EWAS_RESULT clarite-cli-analyze-add-corrected-pvals command line option clarite-cli-analyze-get-significant command line option clarite-cli-plot-manhattan command line option clarite-cli-plot-manhattan-bonferroni command line option clarite-cli-plot-manhattan-fdr command line option

G

GLMRegression (class in clarite.analyze.regression)

I

INPUT clarite-cli-load-from-csv command line option clarite-cli-load-from-tsv command line option

InteractionRegression (class in clarite.analyze.regression)

L

LEFT clarite-cli-modify-merge-variables command line option clarite-cli-modify-move-variables command line option

M

module clarite.analyze clarite.analyze.regression clarite.describe clarite.load clarite.modify clarite.plot clarite.survey

O

OUTCOME clarite-cli-analyze-ewas command line option clarite-cli-analyze-ewas-r command line option OUTPUT clarite-cli-analyze-add-corrected-pvals command line option clarite-cli-analyze-ewas command line option clarite-cli-analyze-ewas-r command line option clarite-cli-analyze-get-significant command line option clarite-cli-describe-correlations command line option clarite-cli-describe-freq-table command line option clarite-cli-describe-get-types command line option clarite-cli-describe-percent-na command line option clarite-cli-describe-skewness command line option clarite-cli-load-from-csv command line option clarite-cli-load-from-tsv command line option clarite-cli-modify-categorize command line option clarite-cli-modify-colfilter command line option clarite-cli-modify-colfilter-min-cat-n command line option clarite-cli-modify-colfilter-min-n command line option clarite-cli-modify-colfilter-percent-zero command line option clarite-cli-modify-drop-extra-categories command line option clarite-cli-modify-make-binary command line option clarite-cli-modify-make-categorical command line option clarite-cli-modify-make-continuous command line option clarite-cli-modify-merge-observations command line option clarite-cli-modify-merge-variables command line option clarite-cli-modify-recode-values command line option clarite-cli-modify-remove-outliers command line option clarite-cli-modify-rowfilter command line option clarite-cli-modify-rowfilter-incomplete-obs command line option clarite-cli-modify-transform-variable command line option clarite-cli-plot-distributions command line option clarite-cli-plot-histogram command line option clarite-cli-plot-manhattan command line option clarite-cli-plot-manhattan-bonferroni command line option clarite-cli-plot-manhattan-fdr command line option

R

Regression (class in clarite.analyze.regression) RIGHT clarite-cli-modify-merge-variables command line option clarite-cli-modify-move-variables command line option

RSurveyRegression (class in clarite.analyze.regression)

T

TOP clarite-cli-modify-merge-observations command line option

TRANSFORM_METHOD clarite-cli-modify-transform-variable command line option

V

VARIABLE clarite-cli-plot-histogram command line option

W

WeightedGLMRegression (class in clarite.analyze.regression)