rare_variant_based_silver_standard: Silver standard based on rare variant association

In liangyy/silver-standard-performance: Generating PR/ROC curves in light and flexible way

Description

Here, we focused on rare variant association evidence reported on height and lipid traits: 1. low-density lipid cholesterol (LDL), 2. high-density lipid cholesterol (HDL), 3. triglycerides (TG), 4. total cholesterol levels (high cholesterol) In particular, we collected significant coding/splicing variants reported previously Marouli et al 2017 and kept variants with effect allele frequency < 0.01 (Table S6: ExomeChip variants with Pdiscovery <2e-07 in the European-ancestry meta-analysis (N=381,625)). Similarly, we collected significant variants reported by Liu et al 2017 (Table S12: Association Results for 444 independently associated variants with lipid traits) and filtered out variants with minor allele frequency < 0.01. For the whole-exome sequencing study conducted in Finnish isolates Locke et al 2019, we extracted significant genes identified by a gene-based test using protein truncating variants (Table S9: Gene-based associations from aggregate testing with EMMAX SKAT-O with P<3.88E-6) and significant variants (Table S7: A review of all variants that pass unconditional threshold of P<5E-07 for at least one trait) with gnomAD MAF < 0.01.

Usage

data(rare_variant_based_silver_standard)

Format

a list of: 1. table: a data.frame with column gene (with Ensembl ID, e.g. ENSG00000084754) , column HPO (HPO term in the format HP:0000512), column EFO (e.g. EFO:0004207), column trait (trait name, e.g. trait) 2. script_info: meta information on how data set is generated.

Source

Source code generating this silver standard dataset

Examples

data(rare_variant_based_silver_standard)
head(rare_variant_based_silver_standard$table)

liangyy/silver-standard-performance documentation built on Dec. 5, 2019, 8:53 a.m.