apply_threshold: Filters GWAS or DE results based on a threshold

In hidecan: Create HIDECAN Plots for Visualising Genome-Wide Association Studies and Differential Expression Results

Filters GWAS or DE results based on a threshold

Description

Filters markers or genes/transcripts based on a threshold applied to their GWAS or DE score, and log2(fold-change) (if applicable). For a set of candidate genes, simply returns the list. Note that markers or genes with a missing score or log2(fold-change) will be removed from the dataset.

Usage

apply_threshold(x, score_thr = 0, log2fc_thr = 0)

## S3 method for class 'GWAS_data'
apply_threshold(x, score_thr = 0, log2fc_thr = 0)

## S3 method for class 'DE_data'
apply_threshold(x, score_thr = 0, log2fc_thr = 0)

## S3 method for class 'CAN_data'
apply_threshold(x, score_thr = 0, log2fc_thr = 0)

## Default S3 method:
apply_threshold(x, score_thr = 0, log2fc_thr = 0)

Arguments

x	Either a GWAS_data, DE_data or CAN_data object.
score_thr	Numeric, threshold to use on markers' or genes/transcripts' score. Only markers or genes with a score equal to or higher than this threshold will be retained. Default value is 0. Ignored for CAN_data.
log2fc_thr	Numeric, threshold to use on the absolute value of genes/ transcripts' log2(fold-change). Only genes/transcripts with an absolute log2(fold-change) equal to or higher than this threshold will be retained. Ignored for GWAS_data and CAN_data.

Value

A filtered tibble (of class GWAS_data_thr, DE_data_thr or CAN_data_thr).

Examples

x <- get_example_data()

## For GWAS results
apply_threshold(GWAS_data(x[["GWAS"]]), score_thr = 4)

## For DE results - in second line, no threshold is applied
## on the log2(fold-change)
apply_threshold(DE_data(x[["DE"]]), score_thr = -log10(0.05), log2fc_thr = 1)
apply_threshold(DE_data(x[["DE"]]), score_thr = -log10(0.05), log2fc_thr = 0)

## No effect on the Candidate genes
apply_threshold(CAN_data(x[["CAN"]]))

hidecan documentation built on Feb. 16, 2023, 6:22 p.m.