make_comorbid_from_optimal: Construct a comorbid PRS from a list of oPRS objects.

Description Usage Arguments Value

Description

Construct a comorbid PRS from a list of oPRS objects.

Usage

1
make_comorbid_from_optimal(oPRS, h_1, phen)

Arguments

bfile

Vector of base file names of the binary file set used for the analysis. See details for construction and instructions.

assoc

Vector of file names and paths to the assoc files with the beta and P values used to construct the score.

p

A vector of P value thresholds to test each score at.

pheno

Vector or file path to phenotype to use for association analysis. This defaults to using the phenotype in the .fam file provided, though you can optionally provide a PLINK style phenotype file.

mode

See details. If mode is set to 1, then P value thresholds are estimated seperately for each of the different scores prior to their combination. If mode is set to 2, then P values thresholds are estimated *all together* to create the optimal score. Mode 2 is significantly slower than mode 1 for obvious reasons.

training

The algorithm used to train the scores. Defaults to 10 times cross validation.

Value

(Currently) A data frame with three columns: FID, IID, and the generated score.


Chris1221/pRs documentation built on May 6, 2019, 11:47 a.m.