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Script arguments

-h, --help

Prints a short help summary with overview of arguments

--morehelp

Print more help on a specific function, or specific functions. Pass the argument name, or argument names (comma seperated), or all for a more detailed description of the whole script and its arguments.

--data

Path to the datafile. This datafile should at least contain the columns FISNumber and age. See :ref:`Creating the input data file`.

--outprefix

Prefix to use for output files.

--extended

Add calculation of extended-pedigree correlations (UncleAunt, AuntNephew, NephewNiece, etc) when used to compute correlations. Generates an extended reformatted pedigree when together with :ref:`--pedigree`

--pedigree

Path to the raw pedigree file, only used when generating a new reformatted pedigree file. See :ref:`Generating a reformatted pedigree file`.

--method

Method for computing correlation, should be Pearson, or Spearman, default is Pearson.

--bivar

Compute bivariate correlations of all combinations of phenotypes. See :ref:`Generating cross-trait correlations`.

--correct

Formula to correct phenotypes before computing correlations. Defaults to no correction

--exclude

Phenotypes for which no correlations should be calculated. For example, when custom covariates are used. Identifier column, age and sex columns are always excluded.

--raw_n

Return an additional .csv file containing the raw number of samples in each kinship in addition to the weighted N file.

--randomsample

Use only 1 pair per family, instead of calculating weighted correlations.

--use_repeated_families

Include all participants from larger families, i.e. don't drop or weigh for duplicate samples or larger families.

--longitudinal

When the input data is of longitudinal nature, this script can perform family-based selection, such that the difference in the year of survey completion among family-members is minimal. If you use this option the input data should contain the columns index (within-subject number of the survey, starting at 1 for fist survey), and Source (string label of the survey). Additionally, you should also add the argument :ref:`--surveycompletion`.

--surveycompletion

Dat file with survey completion years. Should contain the columns FISNumber (identical to datafile), Source (identical to datafile), and invjr (year of survey completion).

Additonal non-argument settings

The top of the Python file contains some additional settings you can tweak. * upper_boundary: Upper age boundary for inclusion in --longitudinal. default = 110 * lower_boundary: Lower age boundary for inclusion in --longitudinal. default = 0 * check_cutoff_drops: save an Age-cutoff_drops.txt file detailing subjects dropped by the cutoffs. default = False * seed: seed for random selection of subjects with --randomsample. default = 1415926536 * explore_plot: Generate scatterplots of each correlation. default = False: * save_separate_data: Store the raw data used for each correlation in separate files. default = False * parallel: Generate reformatted pedigree using multiple processing threads (Currently not working). default = False