suppressPackageStartupMessages(library(GetoptLong))
chr = "chr1"
extend = 50000
windowsize = 6
windowstep = 3
maxwindow = 10000
subgroup = NULL
GetoptLong("config=s", "A configuration R script. Check the help page of `load_config()`
function to find out how to properly set one.",
"chr=s", "A single chromosome name",
"subgroup=s{1,}", "subgroups for test",
"extend=i", "Extension of the gene model, both upstream and downstream. (5kb by default)",
"windowsize=i", "Number CpG sites in a window. (6bp by default)",
"windowstep=i", "Step of the sliding window, measured in number of CpG sites. (3bp by default)",
"maxwindow=i", "Maximum width of a window. (10kb by default)",
head = "Calculate correlation between methylation and gene expression",
foot = "",
script_name = "-e \"epik.cmd::epik()\" correlated_regions")
library(epik)
load_epik_config(config)
if(is.null(subgroup)) {
subgroup = unique(SAMPLE$subgroup)
}
SAMPLE = SAMPLE[SAMPLE$subgroup %in% subgroup, , drop = FALSE]
if(length(unique(SAMPLE$subgroup)) <= 1) {
stop("Number of subgroups is less than 2.")
}
unique_subgroup = unique(SAMPLE$subgroup)
sample_id = rownames(SAMPLE)
if(is.null(EXPR)) stop("'EXPR' should be defined.")
if(is.null(TXDB)) stop("'TXDB' should be defined.")
if(!chr %in% CHROMOSOME) stop("'chr' should be included in 'CHROMOSOME'.")
cr = correlated_regions(sample_id, EXPR, TXDB, chr = chr, subgroup = SAMPLE$subgroup, col = COLOR$subgroup,
window_size = windowsize, window_step = windowstep, max_width = maxwindow, genome = GENOME)
subgroup_str = paste(sort(unique_subgroup), collapse = "_")
dir.create(qq("@{PROJECT_DIR}/rds_cr/@{subgroup_str}"), showWarnings = FALSE)
saveRDS(cr, file = qq("@{PROJECT_DIR}/rds_cr/@{subgroup_str}/cr_@{chr}_@{subgroup_str}.rds"))
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