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Step 1: Get all putative candidate genes for a given sliding window

Source: R/candidate_mining.R
mine_step1.Rd

For a user-defined sliding window relative to each SNP, this function will subset all genes whose genomic positions overlap with the sliding window.

Usage

mine_step1(gene_ranges, marker_ranges, window = 2, expand_intervals = TRUE)

Arguments

gene_ranges

A GRanges object with genomic coordinates of all genes in the genome.

marker_ranges

Genomic positions of SNPs. For a single trait, a GRanges object. For multiple traits, a GRangesList or CompressedGRangesList object, with each element of the list representing SNP positions for a particular trait.

window

Sliding window (in Mb) upstream and downstream relative to each SNP. Default: 2.

expand_intervals

Logical indicating whether or not to expand markers that are represented by intervals. This is particularly useful if users want to use a custom interval defined by linkage disequilibrium, for example. Default: TRUE.

Value

A GRanges or GRangesList object with the genomic positions of all putative candidate genes.

See also

findOverlaps-methods

Examples

data(snp_pos)
data(gene_ranges)
genes <- mine_step1(gene_ranges, snp_pos, window = 2)