Man pages for Bioconductor-mirror/DOQTL
Genotyping and QTL Mapping in DO Mice

addLogAdd two log values.
addLogVectorAdd a vector of log values.
add.missing.F1sAdd Missing F1 Samples
add.sig.thrAdd the significance thresholds to an existing QTL plot.
add.slashAdd a forward slash to a character string.
assoc.mapPerform association mapping on DO mice.
assoc.plotPlot association mapping results.
assoc.scan1Scan one for association mapping.
assoc.scan2Scan two for association mapping.
bayesintFind a Bayesian Credible Interval around a QTL.
calc.genoprobCalculate the founder genotype probabilities at each SNP.
calc.genoprob.allelesCalculate the founder genotype probabilities at each SNP...
calc.genoprob.intensityCalculate the founder genotype probabilities at each SNP.
categorize.variantscategorize.variants
cc.trans.probsTransition probabilities for CC mice.
cluster.strainscluster.strains
coef.doqtlReturn the coefficients of a DOQTL object.
coefplotPlot the QTL model coefficients
colSumsLogSum columns of log transformed data.
condense.model.probsCondense 36 state genotypes down to founder genotypes.
condense.sanger.snpsCreate an HDF5 file with the unique SNP patterns between each...
convert.allele.callsConvert allele calls to numeric values.
convert.genes.to.GRangesConvert MGI genes to GRanges.
convert.genotypesConvert the genotype data from A,C,G,T format to A, H, B, N.
convert.variants.to.GRangesconvert.variants.to.GRanges
convert.variants.to.numericconvert.variants.to.numeric
create.genotype.statesCreate genotype states.
create.html.pageCreate an HTML QTL report
create.Rdata.filesConvert *.txt files to *.Rdata files.
do2sangerImpute the Sanger SNPs onto DO genomes
do.colorsdo.colors
do.statesdo.states
do.trans.probsDetermine DO transition probabilities
emission.probs.alleleCalculate the emission probabilities
estimate.cluster.paramsEstimate genotype cluster means and variances
example.genesexample.genes
example.phenoExample phenotypes.
example.qtlExample QTL.
example.snpsexample.snps
extract.raw.dataExtract intensities, genotypes and call rates from from raw...
fast.qtlrelQTL mapping using QTLRel
fill.in.snpsInterpolate between SNPs at the same cM value.
filter.geno.probsRemove SNPs where the genotype probabilities are too low for...
filter.samplesFALSEilter X, Y and genotype data by call rate
find.overlapping.genesfind.overlapping.genes
gene.plotgene.plot
generic.trans.probsGeneric transition probabilities
genome.plotsPlot the genome of a DO sample.
genome.summary.plotsGenome summary plots
get.chr.lengthsGet chromosome lengths for the mouse
get.do.statesGet the 36 genotype states for the DO
get.gene.nameGet the gene symbol
get.machine.precisionGet the machine precsion
get.max.genoGet the genotype with the highest probability
get.mgi.featuresget.mgi.features
get.num.autoGet the number of autosomes
get.pattern.variantsget.pattern.variants
get.pgwGet the genome wide p-value.
get.sig.thrGet the significance thresholds.
get.strainsget.strains
get.trans.probsGet the transition probabilities between markers.
get.variantsget.variants
hmmHMM function.
html.reportCreate an HTML report for a set of QTL
impute.genotypesImpute Sanger SNPs onto mouse genomes.
intensity.plotsPlot founders and F1 hybrids or genotype state means and...
internal_functionsInternal functions for DOQTL
interpolate.markersinterpolate haplotype or genotype probabilities from one set...
kinshipCreate a kinship matrix.
muga.snps.to.keepSNPs to use for genotyping and mapping on the MUGA
normalize.batchesBatch normalize the X & Y intensity data.
parameter.updateParameter updating in HMM
plot.doqtlPlot a QTL
pxg.plotPhenotype by genotype plot at a single marker.
qtl.heatmapPlot a Heatmap of all QTL
qtl.LRSQTL mapping with no kinship.
qtl.qtlrelUse QTLRel to map a set of traits
qtl.simulateSimulate a QTL in the DO
rankZRank Z transformation
read.vcfRead and parse VCF data
scanonePerform a genome scan.
scanone.assocMap the entire genome using association mapping.
scanone.eqtlMapping using the Matrix EQTL algorithm.
scanone.permPerform a genome scan.
sdp.plotPlot association mapping results.
sex.predictDetermine the sex of each sample
snp.plotsnp.plot
summarize.genotype.transitionsSummarize the genotype data output by the genotyping HMM.
update_from_rUpdate parameters in HMM
variant.plotvariant.plot
write.founder.genomesWrite out the genotypes of DO samples
write.resultsWrite out HMM results.
Bioconductor-mirror/DOQTL documentation built on May 29, 2017, 3:16 a.m.