PRSDS: Get Ploygenic Risk Score

In isglobal-brge/dsOmics: DataSHIELD server site Omic functions

Get Ploygenic Risk Score

Description

Get Ploygenic Risk Score

Usage

PRSDS(resources, snp_threshold, snp_assoc, pgs_id, ...)

Arguments

resources	list of all the VCF resources with biallelic genotype information. It is advised to have one VCF resource per chromosome, a big VCF file with all the information is always slower to use.
snp_threshold	numeric (default 80) Threshold to drop individuals. See details for further information.
...	Corresponds to the prs_table table passed from the client. It is assembled if not NULL.

Details

This function resolves a list of resources subsetting them by the SNPs of risk, this does not ensure that all the SNPs of risk will be found on the data. From all the found SNPs of risk, if an individual has less than 'snp_threshold' (percetage) of SNPs with data, it will be dropped (SNP with no data is marked on the VCF as ./.). If an individual passes this threshold filter but still has SNPs with no data, those SNPs will be counted on the polygenic risk score as non-risk-alleles, to take this infomation into account, the number of SNPs with data for each individual is returned as 'n_snps'.

Value

data.frame were the rownames are the individuals. The columns found are:
prs: Polygenic risk score per individual
prs_nw: Polygenic risk score without weights (weight 1 for each risk allele)
n_snps: Number of SNPs with information for each individual

isglobal-brge/dsOmics documentation built on Nov. 6, 2024, 1:28 a.m.