gQTLstats (version 1.4.2)

manhWngr: manhattan plot with named GRanges

Description

manhattan plot with named GRanges

Usage

manhWngr(store, probeid = "ENSG00000183814.10", sym = "LIN9", fdrsupp, namedGR, slstyle = "NCBI", xlab.in = sym, ylab.in = "-log10 FDR", applyFDRfilter = TRUE)

Arguments

store

instance of ciseStore-class

probeid

name of feature identifier to use for cis association

sym

symbol for feature identifier

fdrsupp

instance of FDRsupp-class

namedGR

GRanges instance with 'name' in mcols element

slstyle

seqlevelsStyle

xlab.in

x axis label

ylab.in

y axis label

applyFDRfilter

if TRUE, use the filter defined in the filterUsed element of the object supplied as fdrsupp on the output

...

additional arguments for plotting

Examples

require(geuvStore2)
require(gQTLBase)
store = makeGeuvStore2()
data(hmm878)
data(filtFDR)
manhWngr(store, fdrsupp=filtFDR, namedGR=hmm878)