mine_step1: Step 1: Get all putative candidate genes for a given sliding...

In almeidasilvaf/cageminer: Candidate Gene Miner

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

Description

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)

almeidasilvaf/cageminer documentation built on Sept. 9, 2023, 5:18 p.m.