score_metagene: Make a metagene from PC Scores.

In PCBS: Principal Component BiSulfite

Make a metagene from PC Scores.

Description

Uses mean binned PC scores across a set of regions to draw a metagene.

Usage

score_metagene(ranks, regions, bin, title, xaxis, yaxis, 
chromDictObj, return.data, linecol)

Arguments

ranks	getPCRanks output data.frame
regions	A three-column data.frame containing a set of regions to test. Columns = chrom, start, end.
bin	integer, number of bins to use in metagenes. Default=100.
title	Output plot title
xaxis	Output plot x-axis title
yaxis	Output plot y-axis title
chromDictObj	Optional chromDictObject made from chromDict(), runs internally if set to NULL (default). Scripts that run this function multiple times will be sped up by setting this option.
return.data	T/F, whether to return a plot, or data that can be run with plot_metagene() or multiple_metagenes().
linecol	Colour for line, auto="red"

Value

If return.data=F, returns a grob containing a metagene plot. Otherwise, returns a list of two data.frames containing metagene and metagene standard error plotting information.

Examples

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

# select chrom, start, and end of all hyper DMRs:
hyper_DMRs <- DMRs[DMRs$FDR <= 0.05 & DMRs$DMR_Zscore > 0,]
regions_hyper <- hyper_DMRs[c(1:3)] 
score_metagene(ranks, regions_hyper)

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