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Simulate number of genes for each sliding window

Source: R/genomic_intervals_operations.R
simulate_windows.Rd

This function counts genes that are contained in sliding windows related to each SNP.

Usage

simulate_windows(
  gene_ranges,
  marker_ranges,
  windows = seq(0.1, 2, by = 0.1),
  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.

windows

Sliding windows (in Mb) upstream and downstream relative to each SNP. Default: seq(0.1, 2, by = 0.1).

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 ggplot object summarizing the results of the simulations.

Details

By default, the function creates 20 sliding windows by expanding upstream and downstream boundaries for each SNP from 0.1 Mb (100 kb) to 2 Mb.

See also

findOverlaps-methods

Examples

data(snp_pos)
data(gene_ranges)
simulate_windows(gene_ranges, snp_pos)