Man pages for gkeele/kqtl
Suite of QTL Mapping Functions
| convert.DOQTL.to.HAPPY | Takes DO-QTL founder haplotype reconstruction output files... |
| extract.r2.interval | Calculate the r^2 (squared correlation coefficient) between... |
| 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.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... |
| 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... |
| pairwise.cor.snp.scan | Calculate the r^2 (squared correlation coefficient) between... |
| 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.threshold.scans | Runs threshold scans from a matrix of outcomes, either... |
| scan.h2lmm | Run a haplotype-based genome scan from probabilities stored... |
| 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... |
