# Genotyping and QTL Mapping in DO Mice

## Documentation for package ‘DOQTL’ version 1.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I K M N P Q R S V W

## -- A --

add.missing.F1s | Add Missing F1 Samples
add.sig.thr | Add the significance thresholds to an existing QTL plot.
add.slash | Add a forward slash to a character string.
addLog | Add two log values.
addLogVector | Add a vector of log values.
assoc.map | Perform association mapping on DO mice.
assoc.map.perms | Perform association mapping on DO mice.
assoc.plot | Plot association mapping results.

## -- B --

batch.normalize | Batch normalize the X & Y intensity data.
bayesint | Find a Bayesian Credible Interval around a QTL.

## -- C --

calc.genoprob | Calculate the founder genotype probabilities at each SNP.
calc.genoprob.alleles | Calculate the founder genotype probabilities at each SNP using allele calls.
calc.genoprob.intensity | Calculate the founder genotype probabilities at each SNP.
categorize.variants | categorize.variants
cc.trans.probs | Transition probabilities for CC mice.
chr.skeletons | Plot the genome of a DO sample.
cluster.strains | cluster.strains
coef.doqtl | Return the coefficients of a DOQTL object.
coefplot | Plot the QTL model coefficients
colSumsLog | Sum columns of log transformed data.
condense.model.probs | Condense 36 state genotypes down to founder genotypes.
condense.sanger.snps | Create an HDF5 file with the unique SNP patterns between each pair of markers.
convert.allele.calls | Convert allele calls to numeric values.
convert.genes.to.GRanges | Convert MGI genes to GRanges.
convert.genotypes | Convert the genotype data from A,C,G,T format to A, H, B, N.
convert.variants.to.GRanges | convert.variants.to.GRanges
convert.variants.to.numeric | convert.variants.to.numeric
create.genotype.states | Create genotype states.
create.html.page | Create an HTML QTL report
create.Rdata.files | Convert *.txt files to *.Rdata files.

## -- D --

do.colors | do.colors
do.states | do.states
do.trans.probs | Determine DO transition probabilities
do2sanger | Impute the Sanger SNPs onto DO genomes
do2sanger.helper | Impute the Sanger SNPs onto DO genomes

## -- E --

estimate.cluster.params | Estimate genotype cluster means and variances
example.genes | example.genes
example.pheno | Example phenotypes.
example.qtl | Example QTL.
example.snps | example.snps
extract.raw.data | Extract intensities, genotypes and call rates from from raw MUGA or MegaMUGA data files

## -- F --

fast.qtlrel | QTL mapping using QTLRel
fill.in.snps | Interpolate between SNPs at the same cM value.
filter.geno.probs | Remove SNPs where the genotype probabilities are too low for one founder state
filter.samples | FALSEilter X, Y and genotype data by call rate
find.overlapping.genes | find.overlapping.genes
founder.F1.intensity.plot | Plot founders and F1 hybrids or genotype state means and variances on an intensity plot.

## -- G --

gene.plot | gene.plot
generic.trans.probs | Generic transition probabilities
genomic.points | Plot the genome of a DO sample.
genotype.by.sample.barplot | Genome summary plots
genotype.by.snp.barplot | Genome summary plots
get.additive | Condense 36 state genotypes down to founder genotypes.
get.chr.lengths | Get chromosome lengths for the mouse
get.do.states | Get the 36 genotype states for the DO
get.dominance | Condense 36 state genotypes down to founder genotypes.
get.full | Condense 36 state genotypes down to founder genotypes.
get.gene.name | Get the gene symbol
get.machine.precision | Get the machine precsion
get.max.geno | Get the genotype with the highest probability
get.mgi.features | get.mgi.features
get.num.auto | Get the number of autosomes
get.pattern.variants | get.pattern.variants
get.pgw | Get the genome wide p-value.
get.sig.thr | Get the significance thresholds.
get.strains | get.strains
get.trans.probs | Get the transition probabilities between markers.
get.variants | get.variants
get.vcf.strains | Read and parse VCF data

## -- H --

html.report | Create an HTML report for a set of QTL

## -- I --

impute.genotypes | Impute Sanger SNPs onto mouse genomes.
intensity.mean.covar.plot | Plot founders and F1 hybrids or genotype state means and variances on an intensity plot.
interpolate.markers | interpolate haplotype or genotype probabilities from one set of markers to another.

## -- K --

keep.homozygotes | Estimate genotype cluster means and variances
kinship.alleles | Create a kinship matrix.
kinship.probs | Create a kinship matrix.

## -- M --

matrixeqtl.snps | Mapping using the Matrix EQTL algorithm.
muga.snps.to.keep | SNPs to use for genotyping and mapping on the MUGA

## -- N --

normalize.batches | Batch normalize the X & Y intensity data.
num.recomb.plot | Summarize the genotype data output by the genotyping HMM.

## -- P --

permutations.qtl.LRS | QTL mapping with no kinship.
plot.doqtl | Plot a QTL
plot.genoprobs | Plot the genome of a DO sample.
prsmth.plot | Plot the genome of a DO sample.
pxg.plot | Phenotype by genotype plot at a single marker.

## -- Q --

qtl.heatmap | Plot a Heatmap of all QTL
qtl.LRS | QTL mapping with no kinship.
qtl.qtlrel | Use QTLRel to map a set of traits
qtl.simulate | Simulate a QTL in the DO
quantilenorm | Batch normalize the X & Y intensity data.

## -- R --

rankZ | Rank Z transformation
read.vcf | Read and parse VCF data
rowSumsLog | Sum columns of log transformed data.

## -- S --

scanone | Perform a genome scan.
scanone.assoc | Map the entire genome using association mapping.
scanone.eqtl | Mapping using the Matrix EQTL algorithm.
scanone.perm | Perform a genome scan.
sdp.plot | Plot association mapping results.
sex.predict | Determine the sex of each sample
snp.plot | snp.plot
summarize.by.samples | Summarize the genotype data output by the genotyping HMM.
summarize.by.snps | Summarize the genotype data output by the genotyping HMM.
summarize.genotype.transitions | Summarize the genotype data output by the genotyping HMM.

## -- V --

variant.plot | variant.plot

## -- W --

write.founder.genomes | Write out the genotypes of DO samples
write.founder.genomes.from.haps | Write out the genotypes of DO samples
write.genoprob.plots | Plot the genome of a DO sample.