simulate_windows {cageminer} | R Documentation |
This function counts genes that are contained in sliding windows related to each SNP.
simulate_windows( gene_ranges, marker_ranges, windows = seq(0.1, 2, by = 0.1), expand_intervals = TRUE )
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. |
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.
A ggplot object summarizing the results of the simulations.
data(snp_pos) data(gene_ranges) simulate_windows(gene_ranges, snp_pos)