\name{manhPlot} \alias{manhPlot} %- Also NEED an '\alias' for EACH other topic documented here. \title{ manhattan plot for an eqtlTests result } \description{ manhattan plot for an eqtlTests result } \usage{ manhPlot(probeid, mgr, ffind, namedlocvec = NULL, locGRanges = NULL, plotter = smoothScatter, tx = function(x) -log10(1 - pchisq(x, 1)), xlab = paste("pos. on ", names(fflist(mgr))[ffind]), ylab = "-log10 p", suppressGeneLoc=FALSE, ...) } %- maybe also 'usage' for other objects documented here. \arguments{ \item{probeid}{ element of colnames of fflist(mgr)[[ffind]] -- the gene of interest, typically } \item{mgr}{ an instance of eqtlTestsManager } \item{ffind}{ index of the ff file of interest -- typically identifying a chromosome where SNP locations define the x-axis of the plot } \item{namedlocvec}{ a vector with named elements, giving SNP locations } \item{locGRanges}{ a GRanges instance with SNP locations } \item{plotter}{ function to be used for rendering } \item{tx}{ the numbers acquired from the manager are assumed to be chi-squared(1) -- this function can be altered to define how the y axis is derived from manager contents } \item{xlab}{ label for x axis } \item{ylab}{ label for y axis } \item{suppressGeneLoc}{ logical; if true, will refrain from trying to indicate gene location on plot. Important to have TRUE when a trans association is being plotted. } \item{\dots}{ passed to plotting function } } %\details{ %%% ~~ If necessary, more details than the description above ~~ %} %\value{ %%% ~Describe the value returned %%% If it is a LIST, use %%% \item{comp1 }{Description of 'comp1'} %%% \item{comp2 }{Description of 'comp2'} %%% ... %} %\references{ %%% ~put references to the literature/web site here ~ %} \author{ VJ Carey } %\note{ %%% ~~further notes~~ %} % %%% ~Make other sections like Warning with \section{Warning }{....} ~ % %\seealso{ %%% ~~objects to See Also as \code{\link{help}}, ~~~ %} \examples{ if (require(SNPlocs.Hsapiens.dbSNP.20100427)) { library(ceuhm3) hm = getSS("ceuhm3", "chr20") library(illuminaHumanv1.db) cptag = get("CPNE1", revmap(illuminaHumanv1SYMBOL)) indc = which(featureNames(hm) == cptag[1]) hm = hm[c(indc,1:19),] # reduce problem hm = hm[chrnum("chr20"),] # reduce snp set td = tempdir() curd = getwd() setwd(td) e1 <- eqtlTests( hm, ~male, targdir="mplex" ) c20 = getSNPlocs("ch20", as.GRanges=TRUE) sr = ranges(c20) sr = GRanges(seqnames="chr20", sr) elementMetadata(sr) = elementMetadata(c20) names(sr) = paste("rs", elementMetadata(sr)$RefSNP_id, sep="") # use ffind=1 below because you have confined attention to chr20 manhPlot( cptag, e1, ffind=1, locGRanges=sr, cex=3) setwd(curd) } } % Add one or more standard keywords, see file 'KEYWORDS' in the % R documentation directory. \keyword{ models }