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.plot              Plot association mapping results.
batch.normalize         Batch normalize the X & Y intensity data.
bayesint                Find a Bayesian Credible Interval around a QTL.
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.
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.Rdata.files      Convert *.txt files to *.Rdata files.
create.genotype.states
                        Create genotype states.
create.html.page        Create an HTML QTL report
do.colors               do.colors
do.states               do.states
do.trans.probs          Determine DO transition probabilities
do2sanger               Impute the Sanger SNPs onto DO genomes
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
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.
gene.plot               gene.plot
generic.trans.probs     Generic transition probabilities
genotype.by.sample.barplot
                        Genome summary plots
get.chr.lengths         Get chromosome lengths for the mouse
get.do.states           Get the 36 genotype states for the DO
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
html.report             Create an HTML report for a set of QTL
impute.genotypes        Impute Sanger SNPs onto mouse genomes.
interpolate.markers     interpolate haplotype or genotype probabilities
                        from one set of markers to another.
kinship.probs           Create a kinship matrix.
muga.snps.to.keep       SNPs to use for genotyping and mapping on the
                        MUGA
plot.doqtl              Plot a QTL
plot.genoprobs          Plot the genome of a DO sample.
pxg.plot                Phenotype by genotype plot at a single marker.
qtl.LRS                 QTL mapping with no kinship.
qtl.heatmap             Plot a Heatmap of all QTL
qtl.qtlrel              Use QTLRel to map a set of traits
qtl.simulate            Simulate a QTL in the DO
rankZ                   Rank Z transformation
read.vcf                Read and parse VCF data
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.genotype.transitions
                        Summarize the genotype data output by the
                        genotyping HMM.
variant.plot            variant.plot
write.founder.genomes   Write out the genotypes of DO samples
