v1.3.0
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Usage
Example Analysis
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Regression
API Reference
CLI Reference
Release History
CLARITE
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Index
Edit on GitHub
Index
Symbols
|
B
|
C
|
D
|
E
|
G
|
I
|
L
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M
|
O
|
R
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T
|
V
|
W
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)
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