simulate_windows: Simulate number of genes for each sliding window

In almeidasilvaf/cageminer: Candidate Gene Miner

Simulate number of genes for each sliding window

Description

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.

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.

Value

A ggplot object summarizing the results of the simulations.

See Also

findOverlaps-methods

Examples

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

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