## ----setup, include=FALSE------------------------------------------------
library("knitr")
## ----eval=FALSE----------------------------------------------------------
# install.packages("DSPRqtl",
# repos = "http://wfitch.bio.uci.edu/R/",
# type = "source")
## ----eval=FALSE----------------------------------------------------------
# install.packages("DSPRqtlDataA",
# repos = "http://wfitch.bio.uci.edu/R/",
# type = "source")
## ----eval=FALSE----------------------------------------------------------
# install.packages("DSPRqtlDataB",
# repos = "http://wfitch.bio.uci.edu/R/",
# type = "source")
## ----eval=FALSE----------------------------------------------------------
# install.packages("DSPRqtlDataA_2.0-1.tar.gz", repos = NULL, type = "source")
# install.packages("DSPRqtlDataB_2.0-1.tar.gz", repos = NULL, type = "source")
## ----eval=FALSE----------------------------------------------------------
# library(DSPRqtlDataA)
## ----eval=FALSE----------------------------------------------------------
# library(DSPRqtlDataB)
## ----eval=FALSE----------------------------------------------------------
# data(A_chromosome.arm_position.in.base.pairs)
## ----eval=FALSE----------------------------------------------------------
# data(A_X_12000000)
# # This gives a data.frame named A_X_12000000
## ------------------------------------------------------------------------
library(DSPRqtl)
data(positionlist_wgenetic)
# This gives a data.frame named poslist
## ------------------------------------------------------------------------
library(DSPRqtl)
## ------------------------------------------------------------------------
data(ADHdata)
# a data.frame named ADHdata
head(ADHdata)
## ----eval=FALSE----------------------------------------------------------
# phenotype.dat <- read.table("/path/to/your/file.txt",
# header = TRUE)
## ----eval=FALSE----------------------------------------------------------
# DSPRscan(model, design, phenotype.dat, id.col, batch, sex)
## ----eval=FALSE----------------------------------------------------------
# data(ADHdata)
# scan.results <- DSPRscan(adh ~ 1,
# design = "inbredA",
# phenotype.dat = ADHdata,
# id.col='patRIL')
## ------------------------------------------------------------------------
data(ADHscan)
## ------------------------------------------------------------------------
ADH.lod.scores <- ADHscan$LODscores
ADH.lod.scores[100:105, ]
## ----eval=FALSE----------------------------------------------------------
# DSPRperm(model, design, phenotype.dat, id.col, batch, niter, alpha, sex)
## ----eval=FALSE----------------------------------------------------------
# perm.test <- DSPRperm(adh ~ 1,
# design = "inbredA",
# phenotype.dat = ADHdata)
## ----eval=FALSE----------------------------------------------------------
# quantile(perm.test$maxLODs, 1 - 0.01)
## ----eval=FALSE----------------------------------------------------------
# DSPRpeaks(qtldat, method, threshold, LODdrop, BCIprob)
## ----echo=FALSE----------------------------------------------------------
load("peaks.rda")
## ----slowchunk, eval=FALSE-----------------------------------------------
# peaks <- DSPRpeaks(ADHscan, threshold = 6.8, LODdrop = 2)
## ------------------------------------------------------------------------
peaks[[26]]
## ----dev="png", fig.width=6.5, fig.height=3.5, fig.cap="Output of `DSPRplot()`"----
DSPRplot(list(ADHscan), threshold=6.8)
## ----eval=FALSE----------------------------------------------------------
# LocalInt(peakChr, peakPos, range, phenotype.dat, pheno.name, design)
## ------------------------------------------------------------------------
# The main QTL
main.peak <- peaks[[26]]
peakChr <- main.peak$peak$chr
peakPos <- main.peak$peak$Ppos
## ----eval=FALSE----------------------------------------------------------
# peak.int <- LocalInt(peakChr,
# peakPos,
# phenotype.dat = ADHdata,
# pheno.name = "adh",
# design = "inbredA")
## ----eval=FALSE----------------------------------------------------------
# DSPRgenos(design, phenotype.dat, id.col, output)
## ----eval=FALSE----------------------------------------------------------
# myGenos <- DSPRgenos(design, phenotype.dat, id.col, output)
# save(myGenos, file = "my file path")
## ----eval=FALSE----------------------------------------------------------
# load(file="my file path")
# # The object will load into the workspace with the same name as
# # when save was used. In this example, this is myGenos.
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