neqtl: Smoothed count of traits mapping to positions across genome
In atbroman/neqtl: Tools for analyzing expression QTL by position on genome

Description Usage Arguments Value Author(s) See Also Examples

Counts the number of positions within a window centered at a position on a chromosome.

Given a list of positions of significant LOD scores, counts the number of traits with significant maximum LOD scores at a given set of positions along the genome

1	neqtl(sigpos.out, chr, pos, win = 5, inc = 0.2)

`sigpos.out`	Output from `maxlod.sigpos` function, a list of positions of significant maximum LOD scores Any list made up of a vector of positions for each chromosome.
`chr`	Vector of chromosomes (as a factor) for count, corresponding to pos, e.g. first column of scanone object
`pos`	Vector of positions for count, corresponding to chr, e.g. second column of scanone object
`win`	Numeric value of window size, count will be number of traits with significant maximum LOD score within the window, centered at c(chr,pos)
`inc`	Numeric value of step increment between positions, default is 0.2

scanone object with cbind(chr,pos) as the first two columns, and number of transcripts with significant maximum LOD score in the pheno column

Karl W. Broman and Aimee Teo Broman

scanone plot.scanone

data(fake.f2expr)
fake.f2expr <- calc.genoprob(fake.f2expr)

## pheno.col=1:nphe(fake.f2expr) takes awhile ##
scan.f2 <- scanone(fake.f2expr,pheno.col=1:100, method="hk")
maxlod.f2 <- maxlod(scan.f2)
sigpos.f2 <- maxlod.sigpos(maxlod.f2,sig.lod=3)

n.f2 <-neqtl(sigpos.f2,chr=scan.f2[,1],pos=scan.f2[,2])
plot(n.f2)