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 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 –pedigree

–pedigree

Path to the raw pedigree file, only used when generating a new reformatted pedigree file. See 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 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 –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