Man pages for gkeele/miqtl
Suite of QTL Mapping Functions
| allele.plotter.whole | Plot the regression coefficients or BLUPs as allele effects... |
| collapse.genomecache | Reduce genome caches by averaging together loci that are very... |
| condition.out.locus.for.scan | Add the residuals to a data.frame after regressing out a... |
| convert.DOQTL.to.HAPPY | Takes DO-QTL founder haplotype reconstruction output files... |
| convert.full.DOQTL.array.to.HAPPY | Takes founder haplotype reconstructions as a 3D array (with... |
| convert.qtl2.to.HAPPY | Takes qtl2geno founder haplotype reconstruction output files... |
| extract.chr.max.statistics.from.genomewide | Extracts chromosome-level statistics from the full output of... |
| extract.mediation.expression.qr | Pre-compute QR decompositions from genome cache for efficient... |
| extract.mediation.qr | Pre-compute QR decompositions from genome cache for efficient... |
| extract.qr | Pre-compute QR decompositions from genome cache for efficient... |
| extract.r2.interval | Calculate the r^2 (squared correlation coefficient) between... |
| generate.qr.permutation.index.matrix | Outputs a matrix of permuted indeces for permutation scans,... |
| generate.sample.outcomes.matrix | Returns a matrix of outcome samples, either permutations or... |
| generate.simple.sample.outcomes.matrix | Returns a matrix of outcome samples, either permutations of... |
| genome.plotter.chr | Plot single chromosome windows of haplotype-based genome scan |
| genome.plotter.region | Plot user-specified windows of haplotype-based and snp-based... |
| genome.plotter.to.pdf | Plot whole genome and single chromosome windows of... |
| genome.plotter.whole | Plot one or more haplotype-based genome scans flexibly (whole... |
| get.gev.thresholds | Returns a significance threshold based on fitting max LODs or... |
| grab.locus.from.scan | Pulls loci from scan objects based on specified criteria |
| imputed.snp.scan.h2lmm | Run a SNP-based genome scan from probabilities stored in a... |
| instability.lm.scan | Runs quick fixed effect only scans off of simple bootstrap... |
| lmmbygls | Run a haplotype-based genome scan from probabilities stored... |
| mediation.scan.qr | Runs genome-wide mediation scan from a QR decomposition... |
| pairwise.cor.snp.scan | Calculate the r^2 (squared correlation coefficient) between... |
| plot_locus.effect.from.scan | Plot the regression coefficients as allele effects for a... |
| prob.heatmap | Plot founder haplotype dosages/probabilities, ordered by... |
| rint | Returns the rank-based inverse normal transformation |
| run.positional.scans | Run single chromosome scans on parametric bootstrap samples... |
| run.qr.permutation.threshold.mediation.expression.scans | Runs mediation permutation scans for significance thresholds... |
| run.qr.permutation.threshold.mediation.scans | Runs mediation permutation scans for significance thresholds... |
| run.qr.permutation.threshold.scans | Runs permutation scans for significance thresholds based on... |
| run.simple.permutation.threshold.scans | Runs threshold scans from a matrix of permutation indexes |
| run.threshold.scans | Runs threshold scans from a matrix of outcomes, either... |
| scan.h2lmm | Run a haplotype-based genome scan from probabilities stored... |
| scan.qr | Runs genome scan from a QR decomposition object and phenotype... |
| single.chr.plotter.w.ci | Plot whole genome and single chromosome windows of... |
| snp.genome.plotter.whole | Plot whole genome and single chromosome windows of a... |
| snp.genome.plotter.w.r2 | Plot a single chromosome window of a SNP-based genome scan... |
