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DOQTL
QTL mapping for Diversity Outbred mice (and other multi-founder advanced intercrosses)
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Version
Version
1.8.0
1.6.0
1.2.0
1.0.0
Version
1.8.0
License
GPL-3
Maintainer
Daniel Gatti
Last Published
December 7th, 2012
Functions in DOQTL (1.8.0)
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do.colors
do.colors
create.html.page
Create an HTML QTL report
convert.genotypes
Convert the genotype data from A,C,G,T format to A, H, B, N.
filter.samples
FALSEilter X, Y and genotype data by call rate
example.pheno
Example phenotypes.
impute.genotypes
Impute Sanger SNPs onto mouse genomes.
filter.geno.probs
Remove SNPs where the genotype probabilities are too low for one founder state
plot.doqtl
Plot a QTL
write.founder.genomes
Write out the genotypes of DO samples
addLog
Add two log values.
convert.variants.to.GRanges
convert.variants.to.GRanges
get.mgi.features
get.mgi.features
coef.doqtl
Return the coefficients of a DOQTL object.
get.pgw
Get the genome wide p-value.
get.max.geno
Get the genotype with the highest probability
get.variants
get.variants
calc.genoprob.intensity
Calculate the founder genotype probabilities at each SNP.
convert.allele.calls
Convert allele calls to numeric values.
muga.snps.to.keep
SNPs to use for genotyping and mapping on the MUGA
fast.qtlrel
QTL mapping using QTLRel
qtl.LRS
QTL mapping with no kinship.
get.trans.probs
Get the transition probabilities between markers.
scanone
Perform a genome scan.
sex.predict
Determine the sex of each sample
assoc.scan2
Scan two for association mapping.
create.genotype.states
Create genotype states.
condense.sanger.snps
Create an HDF5 file with the unique SNP patterns between each pair of markers.
example.qtl
Example QTL.
batch.normalize
Batch normalize the X & Y intensity data.
get.pattern.variants
get.pattern.variants
addLogVector
Add a vector of log values.
assoc.map
Perform association mapping on DO mice.
plot.genoprobs
Plot the genome of a DO sample.
estimate.cluster.params
Estimate genotype cluster means and variances
read.vcf
Read and parse VCF data
gene.plot
gene.plot
sdp.plot
Plot association mapping results.
cluster.strains
cluster.strains
generic.trans.probs
Generic transition probabilities
emission.probs.allele
Calculate the emission probabilities
variant.plot
variant.plot
qtl.qtlrel
Use QTLRel to map a set of traits
calc.genoprob.alleles
Calculate the founder genotype probabilities at each SNP using allele calls.
cc.trans.probs
Transition probabilities for CC mice.
snp.plot
snp.plot
qtl.simulate
Simulate a QTL in the DO
get.gene.name
Get the gene symbol
intensity.plots
Plot founders and F1 hybrids or genotype state means and variances on an intensity plot.
find.overlapping.genes
find.overlapping.genes
get.num.auto
Get the number of autosomes
convert.genes.to.GRanges
Convert MGI genes to GRanges.
scanone.assoc
Map the entire genome using association mapping.
create.Rdata.files
Convert *.txt files to *.Rdata files.
convert.variants.to.numeric
convert.variants.to.numeric
do2sanger
Impute the Sanger SNPs onto DO genomes
kinship.probs
Create a kinship matrix.
parameter.update
Parameter updating in HMM
summarize.genotype.transitions
Summarize the genotype data output by the genotyping HMM.
condense.model.probs
Condense 36 state genotypes down to founder genotypes.
do.states
do.states
do.trans.probs
Determine DO transition probabilities
genome.summary.plots
Genome summary plots
interpolate.markers
interpolate haplotype or genotype probabilities from one set of markers to another.
add.missing.F1s
Add Missing F1 Samples
assoc.plot
Plot association mapping results.
hmm
HMM function.
bayesint
Find a Bayesian Credible Interval around a QTL.
internal_functions
Internal functions for DOQTL
rankZ
Rank Z transformation
qtl.heatmap
Plot a Heatmap of all QTL
colSumsLog
Sum columns of log transformed data.
pxg.plot
Phenotype by genotype plot at a single marker.
example.genes
example.genes
get.chr.lengths
Get chromosome lengths for the mouse
get.machine.precision
Get the machine precsion
update_from_r
Update parameters in HMM
scanone.perm
Perform a genome scan.
html.report
Create an HTML report for a set of QTL
scanone.eqtl
Mapping using the Matrix EQTL algorithm.
assoc.scan1
Scan one for association mapping.
add.slash
Add a forward slash to a character string.
add.sig.thr
Add the significance thresholds to an existing QTL plot.
coefplot
Plot the QTL model coefficients
categorize.variants
categorize.variants
example.snps
example.snps
get.do.states
Get the 36 genotype states for the DO
extract.raw.data
Extract intensities, genotypes and call rates from from raw MUGA or MegaMUGA data files
get.strains
get.strains
get.sig.thr
Get the significance thresholds.
fill.in.snps
Interpolate between SNPs at the same cM value.
calc.genoprob
Calculate the founder genotype probabilities at each SNP.
write.results
Write out HMM results.