Man pages for gkeele/miqtl
Suite of QTL Mapping Functions

allele.plotter.wholePlot the regression coefficients or BLUPs as allele effects...
collapse.genomecacheReduce genome caches by averaging together loci that are very...
condition.out.locus.for.scanAdd the residuals to a data.frame after regressing out a...
convert.DOQTL.to.HAPPYTakes DO-QTL founder haplotype reconstruction output files...
convert.full.DOQTL.array.to.HAPPYTakes founder haplotype reconstructions as a 3D array (with...
convert.qtl2.to.HAPPYTakes qtl2geno founder haplotype reconstruction output files...
extract.qrPre-compute QR decompositions from genome cache for efficient...
extract.r2.intervalCalculate the r^2 (squared correlation coefficient) between...
generate.qr.permutation.index.matrixOutputs a matrix of permuted indeces for permutation scans,...
generate.sample.outcomes.matrixReturns a matrix of outcome samples, either permutations or...
generate.simple.sample.outcomes.matrixReturns a matrix of outcome samples, either permutations of...
genome.plotter.chrPlot single chromosome windows of haplotype-based genome scan
genome.plotter.regionPlot user-specified windows of haplotype-based and snp-based...
genome.plotter.to.pdfPlot whole genome and single chromosome windows of...
genome.plotter.wholePlot one or more haplotype-based genome scans flexibly (whole...
get.gev.thresholdsReturns a significance threshold based on fitting max LODs or...
grab.locus.from.scanPulls loci from scan objects based on specified criteria
imputed.snp.scan.h2lmmRun a SNP-based genome scan from probabilities stored in a...
instability.lm.scanRuns quick fixed effect only scans off of simple bootstrap...
lmmbyglsRun a haplotype-based genome scan from probabilities stored...
pairwise.cor.snp.scanCalculate the r^2 (squared correlation coefficient) between...
prob.heatmapPlot founder haplotype dosages/probabilities, ordered by...
rintReturns the rank-based inverse normal transformation
run.positional.scansRun single chromosome scans on parametric bootstrap samples...
run.qr.permutation.threshold.scansRuns permutation scans for significance thresholds based on...
run.simple.permutation.threshold.scansRuns threshold scans from a matrix of permutation indexes
run.threshold.scansRuns threshold scans from a matrix of outcomes, either...
scan.h2lmmRun a haplotype-based genome scan from probabilities stored...
scan.qrRuns genome scan from a QR decomposition object and phenotype...
single.chr.plotter.w.ciPlot whole genome and single chromosome windows of...
snp.genome.plotter.wholePlot whole genome and single chromosome windows of a...
snp.genome.plotter.w.r2Plot a single chromosome window of a SNP-based genome scan...
gkeele/miqtl documentation built on Nov. 19, 2017, 5:47 a.m.