construct_score: Construct a Simple Polygenic Risk Score
In Chris1221/pRs: Polgenic Risk Score Toolkit in R

Description Usage Arguments Details Value

Given input genetic files and association statistics, generate one of a number of polygenic risk scores.

1 2	construct_score(file = NULL, assoc = NULL, alternate_weights = NULL, mode = "single", p = 0.05)

`file`	Path to converted raw plink file. This is a typical `plink` file which has been converted to an R readable format through `recodeA`. See `details` for specific conversion instructions.
`assoc`	File path to summary statistics used for score construction. This file must contain a column named "P" or "pvalue" or "p-value" or something similar. If the beta coefficients are to be used from this file (as opposed to `alternate_weights`) then a column named "beta", "Beta", "B", or similar must be present. See `details` for more information.
`alternate_weights`	File path to an alternate weighting scheme for use in cross-disorder PRS.
`mode`	One of "single" or "multiple". For more details see `details`.
`p`	P value cutoff for SNP inclusion in PRS.

This is helper code to construct a simple PRS in R. Note that it is currently unoptimized, meaning that it is currently implimented in R and not RcppArmadillo as it will be in the future.

In order to use this function, you must convert your genetic files to be plink.raw format. This serves several purposes:

It allows this function to have a standard set of inputs which are predictable and easy to deal with.
It is an efficient format which is easy to deal with computationally.
Avoids any shell integration, which makes the functions more cross-platform.

We understand that this represents an additional processing step, but we think that the reward is worth the time. If you've done this kind of thing before, please use the --recodeA flag to produce a single plink.raw file. If you have not, we have provided a vignette on data conversion and the same information in the package wiki online.
If mode == "single", then the function assumes that you wish to construct the scores using weighting coefficients from the *same disorder* (i.e. using the weights provided in the assoc file) and those P values for thresholding. If mode == "multiple" then the function assumes that you wish to use the original P values in assoc to perform SNP selection, but an alternate set of weights. Provide this alternate set of weights through alternate_weights.

The inclusion criteria for the score are provided with the p arguement. All variants with P < p will be included in the score.

An S4 PRS object. Slots include: