plot_metagene: Generate a metagene plot from raw metagene data.

In PCBS: Principal Component BiSulfite

Generate a metagene plot from raw metagene data.

Description

Plots a metagene object using the raw data generated by score_metagene().

Usage

plot_metagene(data, title, xaxis, yaxis, linecol)

Arguments

data	list, score_metagene() raw data output
title	Output plot title
xaxis	Output plot x-axis title
yaxis	Output plot y-axis title
linecol	Colour for line, auto="red"

Value

Returns a grob containing a plot of the input metagene data.

Examples

ranks <- getPCRanks(eigen, IDs = c("trt", "ctl"), PC = 1)
DMRs <- Get_Novel_DMRs(ranks, 2940, minCpGs=10)

# Select all significantly hypomethylated DMRs:
hypo_DMRs <- DMRs[DMRs$FDR <= 0.05 & DMRs$DMR_Zscore < 0,] 

# select chrom, start, and end of all hyper DMRs
regions_hypo <- hypo_DMRs[c(1:3)] 

# return.data = T returns raw data instead of a plot:
hypo_metagene <- score_metagene(ranks, regions_hypo, return.data = TRUE)

plot_metagene(hypo_metagene)

PCBS documentation built on Sept. 11, 2024, 6:11 p.m.