manhattanDMCs-method {DMCHMM}R Documentation

manhattanDMCs method

Description

Creates a Manhattan plot based on the p-values obtained from findDMCs method

Usage

manhattanDMCs(object, col, chrlabs, suggestiveline, genomewideline, highlight,
  logp, annotatePval, annotateTop, ...)

## S4 method for signature 'BSDMCs'
manhattanDMCs(object, col, chrlabs, suggestiveline,
  genomewideline, highlight, logp, annotatePval, annotateTop, ...)

Arguments

object

A BSData-class or BSDMCs-class object

col

A character vector indicating which colors to alternate.

chrlabs

A character vector equal to the number of chromosomes specifying the chromosome labels (e.g., c(1:22, "X", "Y", "MT")).

suggestiveline

Where to draw a "suggestive" line. Default -log10(1e-5). Set to FALSE to disable.

genomewideline

Where to draw a "genome-wide sigificant" line. Default -log10(5e-8). Set to FALSE to disable.

highlight

A character vector of SNPs in your dataset to highlight. These SNPs should all be in your dataset.

logp

If TRUE, the -log10 of the p-value is plotted. It isn't very useful to plot raw p-values, but plotting the raw value could be useful for other genome-wide plots, for example, peak heights, bayes factors, test statistics, other "scores," etc.

annotatePval

If set, SNPs below this p-value will be annotated on the plot.

annotateTop

If TRUE, only annotates the top hit on each chromosome that is below the annotatePval threshold.

...

other possible parameters

Value

A Manhattan plot

Author(s)

Farhad Shokoohi <shokoohi@icloud.com>

Examples

set.seed(1980)
nr <- 150; nc <- 8
metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr)
methc <- matrix(rbinom(n=nr*nc,c(metht),prob = runif(nr*nc)),nr,nc)
r1 <- GRanges(rep('chr1', nr), IRanges(1:nr, width=1), strand='*')
names(r1) <- 1:nr
cd1 <- DataFrame(Group=rep(c('G1','G2'),each=nc/2),row.names=LETTERS[1:nc])
OBJ1 <- cBSData(rowRanges=r1,methReads=methc,totalReads=metht,colData=cd1)
OBJ2 <- methHMEM(OBJ1, MaxK=2, mc.cores=2)
OBJ3 <- methHMMCMC(OBJ2, mc.cores=2)
OBJ4 <- findDMCs(OBJ3, mc.cores=2)
manhattanDMCs(OBJ4)

[Package DMCHMM version 1.2.0 Index]