fake.annot: Simulated annotation for fake.f2expr cross

In atbroman/neqtl: Tools for analyzing expression QTL by position on genome

Description

Annotation data for fake.f2expr expression traits denoting position on the genome.

Usage

data(fake.annot)

Format

A data.frame with a column for chromosome (chr, as factor), and position (pos, as numeric)

Details

There are 1000 simulated positions, one corresponding to each expression trait

Examples

## Not run: 
library(qtl)

# random seed
set.seed(5297830)

# load map
data(map10)

# drop X chr
map10 <- map10[-20]

# chromosome lengths
L <- summary(map10)[1:19,"length"]
names(L) <- as.character(1:19)

# simulate genes in different positions
n.genes <- 1000
chr <- factor(sample(names(L), n.genes, prob=L/sum(L), repl=TRUE), levels=1:19)
pos <- runif(n.genes, 0, L[chr])
genenam <- paste("gene", 1:n.genes, sep="")
genes <- data.frame(chr=chr, pos=pos)
rownames(genes) <- genenam


# which ones have cis?
cis <- sample(c(FALSE,TRUE), n.genes, prob=c(9,1), repl=TRUE)

# trans eqtl on chr 1 at 50 cM
trans <- sample(c(FALSE,TRUE), n.genes, prob=c(8,2), repl=TRUE)
trans[cis] <- FALSE # make cis ones be not trans

# cis effects
cis.eff <- runif(n.genes, 0.2, 4.9)
cis.eff[!cis] <- 0

# trans effects
trans.eff <- runif(n.genes, 0.2, 0.9)
trans.eff[!trans] <- 0

# simulate annotation
fake.annot <- data.frame(chr=factor(sample(names(L),
           n.genes, prob=L/sum(L), repl=TRUE), levels=1:19),
           pos=runif(n.genes, 0, L[chr]),row.names=genenam)
fake.annot[cis,"chr"] <- genes[cis,"chr"]
fake.annot[cis,"pos"] <-
  apply(cbind(genes[cis,"pos"]+runif(sum(cis),min=-2.5,max=2.5),
        L[genes[cis,"chr"]]),1,function(x) max(0,min(x)))

#save(fake.annot,file="neqtl/data/fake.annot.RData")

## End(Not run)
data(fake.annot)

atbroman/neqtl documentation built on May 10, 2019, 2:08 p.m.