Nothing
## ---- eval=TRUE, include=TRUE, echo=FALSE--------------------------------
#just to be sure
library("detectRUNS")
## ------------------------------------------------------------------------
genotypeFilePath <- system.file(
"extdata", "Kijas2016_Sheep_subset.ped", package="detectRUNS")
mapFilePath <- system.file(
"extdata", "Kijas2016_Sheep_subset.map", package="detectRUNS")
## ----results='hide',message=FALSE, cache=FALSE, warning=FALSE------------
slidingRuns <- slidingRUNS.run(
genotypeFile = genotypeFilePath,
mapFile = mapFilePath,
windowSize = 15,
threshold = 0.05,
minSNP = 20,
ROHet = FALSE,
maxOppWindow = 1,
maxMissWindow = 1,
maxGap = 10^6,
minLengthBps = 250000,
minDensity = 1/10^3, # SNP/kbps
maxOppRun = NULL,
maxMissRun = NULL
)
## ----results='hide',message=FALSE, cache=FALSE, warning=FALSE------------
consecutiveRuns <- consecutiveRUNS.run(
genotypeFile =genotypeFilePath,
mapFile = mapFilePath,
minSNP = 20,
ROHet = FALSE,
maxGap = 10^6,
minLengthBps = 250000,
maxOppRun = 1,
maxMissRun = 1
)
## ----results='hide',message=FALSE, cache=FALSE, warning=FALSE------------
slidingRuns_het <- slidingRUNS.run(
genotypeFile = genotypeFilePath,
mapFile = mapFilePath,
windowSize = 10,
threshold = 0.05,
minSNP = 10,
ROHet = TRUE,
maxOppWindow = 2,
maxMissWindow = 1,
maxGap = 10^6,
minLengthBps = 10000,
minDensity = 1/10^6, # SNP/kbps
maxOppRun = NULL,
maxMissRun = NULL
)
## ----results='hide',message=FALSE, cache=FALSE---------------------------
consecutiveRuns_het <- consecutiveRUNS.run(
genotypeFile =genotypeFilePath,
mapFile = mapFilePath,
minSNP = 10,
ROHet = TRUE,
maxGap = 10^6,
minLengthBps = 10000,
maxOppRun = 2,
maxMissRun = 1
)
## ---- results='hide',message=FALSE, cache=FALSE--------------------------
summaryList <- summaryRuns(
runs = slidingRuns, mapFile = mapFilePath, genotypeFile = genotypeFilePath,
Class = 6, snpInRuns = TRUE)
## ------------------------------------------------------------------------
summaryList$summary_ROH_count
## ------------------------------------------------------------------------
summaryList$summary_ROH_mean_chr
## ------------------------------------------------------------------------
head(summaryList$SNPinRun)
## ---- fig.show='hold', fig.cap="Plot runs per individual"----------------
plot_Runs(runs = slidingRuns)
## ---- fig.show='hold', fig.cap="Plot runs per individual", message=FALSE, cache=FALSE, warning=FALSE, results='hide'----
plot_StackedRuns(runs = slidingRuns)
## ---- fig.show='hold', message=FALSE, cache=FALSE, warning=FALSE, results='hide',fig.width=6,fig.height=4----
plot_SnpsInRuns(
runs = slidingRuns[slidingRuns$chrom==2,], genotypeFile = genotypeFilePath,
mapFile = mapFilePath)
## ---- fig.show='hold', message=FALSE, cache=FALSE, warning=FALSE, results='hide',fig.width=6,fig.height=4----
plot_SnpsInRuns(
runs = slidingRuns[slidingRuns$chrom==24,], genotypeFile = genotypeFilePath,
mapFile = mapFilePath)
## ----message=FALSE, cache=FALSE, results='hide'--------------------------
topRuns <- tableRuns(
runs = slidingRuns, genotypeFile = genotypeFilePath, mapFile = mapFilePath,
threshold = 0.7)
## ----echo=FALSE----------------------------------------------------------
print(topRuns)
## ---- message=FALSE, cache=FALSE, results='hide', fig.width=6,fig.height=4----
plot_manhattanRuns(
runs = slidingRuns[slidingRuns$group=="Jacobs",],
genotypeFile = genotypeFilePath, mapFile = mapFilePath)
## ---- echo=FALSE, message=FALSE, cache=FALSE-----------------------------
head(
Froh_inbreeding(runs = slidingRuns,mapFile = mapFilePath,genome_wide = TRUE))
## ---- echo=FALSE, message=FALSE, cache=FALSE, fig.width=5, fig.height=4----
plot_InbreedingChr(
runs = slidingRuns, mapFile = mapFilePath, style = "FrohBoxPlot")
## ---- message=FALSE------------------------------------------------------
savedRunFile <- system.file(
"extdata", "Kijas2016_Sheep_subset.sliding.csv", package="detectRUNS")
runs <- readExternalRuns(inputFile = savedRunFile, program = "detectRUNS")
head(runs)
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