In perishky/ewaff: Efficient and Flexible EWAS

Genome-wide methylation analysis report

• study: r study
• author: r author
• date: r format(Sys.time(), '%d %B, %Y')

Parameters

object$parameters

out <- NULL
if (!is.null(object$sample.characteristics)) {
    out <- knit_child(file.path(report.path, "sample-characteristics.rmd"))
}

if (!is.null(out))
    cat(out, sep="\n\n")

out <- NULL
if (!is.null(object$covariate.associations)) {
    out <- knit_child(file.path(report.path, "covariate-associations.rmd"))
}

if (!is.null(out))
    cat(out, sep="\n\n")

out <- NULL
if (!is.null(object$additional.associations)) {
    out <- knit_child(file.path(report.path, "additional-associations.rmd"))
}

if (!is.null(out))
    cat(out, sep="\n\n")

QQ plots

plot <- object$qq.plot
out <- knit_child(file.path(report.path, "qq-plot.rmd"))

cat(out, sep="\n")

Manhattan plots

plot <- object$manhattan.plot
out <- knit_child(file.path(report.path, "manhattan-plot.rmd"))

cat(out, sep="\n")

Significant CpG sites

There were r length(object$significant.sites) CpG sites with association p-values < r object$parameters$sig.threshold. These are listed in the file associations.csv.

tab <- with(object, cpg.stats[match(significant.sites, rownames(cpg.stats)),])
write.csv(tab, file=file.path(opts_knit$get("output.dir"), "associations.csv"))

practical.sites <- object$practical.sites
tab <- with(object, cpg.stats[match(practical.sites, rownames(cpg.stats)),])

Below are the r length(practical.sites) CpG sites with association p-values < r object$parameters$practical.threshold in the r object$parameters$model regression model.

knitr::kable(tab)

Plots of these sites follow, one for each covariate set. "p[lm]" denotes the p-value obtained using a linear model and "p[beta]" the p-value obtained using beta regression.

out <- NULL
for (cpg in practical.sites) 
    out <- c(out, knit_child(file.path(report.path, "cpg-plot.rmd")))

cat(out, sep="\n")

Selected CpG sites

Number of CpG sites selected: r length(object$selected.sites).

tab <- with(object, cpg.stats[match(selected.sites, rownames(cpg.stats)),])
knitr::kable(tab)

out <- NULL
for (cpg in object$selected.sites)
    out <- c(out, knit_child(file.path(report.path, "cpg-plot.rmd")))

cat(out, sep="\n\n")

R session information

sessionInfo()

perishky/ewaff documentation built on Nov. 10, 2024, 4:53 p.m.