prs_mergeR: Creates model for pathway regressed against end-point omics

In Sabor117/PathWAS: Creates predictive models of biological pathway functionality

Creates model for pathway regressed against end-point omics

Description

prs_mergeR is a lower level function for pathWAS_predictR which merges a data frame of PRS for a given pathway and a data frame of selected omics (and the name of the end-point) and then performs a regression on this merged data frame.

Usage

prs_mergeR(pathway_scores, omics, gene)

Arguments

pathway_scores	data frame. At LEAST 2 columns: MUST contain "iid" column. Every other column is either individual gene PRS or a summed pathway PRS in one column
omics	data frame. ONLY 2 columns. MUST contain "iid" column overlapping with pathway_scores. Other column is the end-point omics.
gene	character. Name of the end-point protein used in the analysis.

Details

In pathWAS_predictR this function is used to merge two data frames. One data frame is 2 columns: IID and pathway PRS (where pathway PRS is a summed PRS for every gene PRS in the pathway). The second data frame is also 2 columns: IID and the proteomics measurements for your selected end-point. The function will merge these two data frames by IID and then regresses the omics values by the summed PRS. To function correctly the IIDs must overlap between both data frames (I.e. PRS must be made in the same individuals for which you have your end-point omics).

Sabor117/PathWAS documentation built on Nov. 29, 2024, 7:44 a.m.