A B C D E F G H I K M N P Q R S V W
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. |
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. |
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. |
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 |
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 |
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 |
html.report | Create an HTML report for a set of QTL |
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. |
keep.homozygotes | Estimate genotype cluster means and variances |
kinship.alleles | Create a kinship matrix. |
kinship.probs | Create a kinship matrix. |
matrixeqtl.snps | Mapping using the Matrix EQTL algorithm. |
muga.snps.to.keep | SNPs to use for genotyping and mapping on the MUGA |
normalize.batches | Batch normalize the X & Y intensity data. |
num.recomb.plot | Summarize the genotype data output by the genotyping HMM. |
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. |
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. |
rankZ | Rank Z transformation |
read.vcf | Read and parse VCF data |
rowSumsLog | Sum columns of log transformed 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.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. |
variant.plot | variant.plot |
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. |