| apply.filters | Drop samples and/or markers flagged as low-quality |
| argyle | argyle: An 'R' package for import and QC of genotypes from... |
| as.data.frame.genotypes | Convert genotypes to a dataframe |
| as.genotypes | Convert an 'R/qtl' object to a 'genotypes' object |
| as.rqtl | Convert a 'genotypes' object to an 'R/qtl' object |
| assoc.plink | Perform a genome-wide association scan with PLINK |
| autosomes | Shortcut for grabbing just the autosomes |
| bafplot | Plot B-allele frequency (BAF) and log2-intensity ratio (LRR)... |
| blank.grob | Make a blank grob for plotting |
| cash-.genotypes | Access attributes of a 'genotypes' object as if they were a... |
| cbind.genotypes | Concatenate two 'genotypes' objects 'horizontally' |
| consensus | Identify the consensus genotype call among a group of samples |
| dist.genotypes | Calculate a simple genetic distance: proportion of alleles... |
| dotplot.genotypes | Show a visual representation of a slice of a genotype matrix |
| drop.intensity | Strip intensity matrices from a 'genotypes' object |
| ex | Genotype calls and intensities from the GigaMUGA array for... |
| export.doqtl | Export genotyping result in format suitable for DOQTL |
| filter.plink | Filter markers and samples from a dataset with PLINK |
| filters.genotypes | Get filters attached to a 'genotypes' object |
| fixed.diffs | Identify fixed differences between a pair of samples |
| fix.strand.swaps | Fix alleles in marker map using those in observed genotypes |
| freq | Calculate allele frequencies by marker or sample |
| freqplot | Plot frequencies of missing, heterozygous, and minor-allele... |
| genoapply | Apply a function over a 'genotypes' object, by sample or... |
| genotypes | Constructor for a 'genotypes' object |
| get.baf | Extract BAF/LRR as a dataframe |
| get.call | Extract genotype calls as a dataframe |
| get.intensity | Extract hybridization intensities as a dataframe |
| ggmanhattan | Create skeleton of a 'Manhattan plot' (concatenated... |
| guess.parents | Attempt to guess the mother-father pair corresponding to... |
| has.intensity | Check if a 'genotypes' object has intensity data attached |
| head.genotypes | Show the first few samples and markers for a 'genotypes' |
| heatmap.genotypes | Plot a heatmap representing genetic distances between samples |
| heterozygosity | Calculate heterozygosity by marker |
| informative | Find markers informative between sample groups |
| intensity.genotypes | Get intensity matrices attached to a 'genotypes' object |
| intensityhist | Plot histogram of (sum-)intensities by sample |
| intensity.vs.ref | KS-test for difference in intensity distributions |
| is.filtered | Check if markers or samples are marked with filters |
| kinship.plink | Compute realized kinship matrix (aka GRM) with PLINK |
| ld.plink | Compute pairwise LD between markers with PLINK |
| maf | Calculate minor-allele frequency (MAFs) from a genotypes... |
| markers.genotypes | Get marker map for a 'genotypes' object |
| mds.plink | Perform classical multidimensional scaling (MDS) with PLINK |
| mendel.distance | Compute rate of Mendelian inconsistency between an individual... |
| merge.genotypes | Merge two 'genotypes' objects which share markers |
| missingness | Calculate rate of missing genoypes by marker or sample |
| nmiss | Count number of missing genotypes by marker or sample |
| oneway | Get one-way marker-phenotype association |
| oneway.plot | Make graphical representation of a 'one-way'... |
| pca.genotypes | Perform PCA on a 'genotypes' object |
| pca.plink | Perform PCA on genotypes with PLINK |
| plinkify | Create a pointer to a PLINK fileset |
| plot.clusters | Plot 2D hybridization intensities at a few markers |
| plot.haplotypes | Plot the results of haplotype reconstruction |
| plot.pca.result | Auto-plotting of a PCA result |
| predict.f1 | Predict genotype of an F1 individual given genotypes of its... |
| predict.haplogroup | Predict haplogroup (eg chrY or chrM), given labelled controls |
| predict.sex | Predict sample sexes based on genotype and intensity data |
| prop.het | Calculate the proportion of sites at which each sample is... |
| prune.plink | Prune markers by pairwise LD with PLINK |
| qcplot | Produce a visual summary of QC measures |
| quantile.normalize | Perform quantile normalization of intensity data. |
| rbind.genotypes | Concatenate two 'genotypes' objects 'vertically' |
| read.beadstudio | Read genotype calls and hybridization from Illumina... |
| read.plink | Read a PLINK binary fileset into a 'genotypes' object |
| recode.genotypes | Switch between character and numeric representations of... |
| recode.to.parent | Recode genotypes against genotypes of a parent |
| reconstruct.haps | Perform (simplistic) haplotype reconstruction, given parental... |
| replace.map | Swap out the marker map for a different one |
| replace.names | Rename some or all samples |
| run.marker.qc | Perform basic marker-wise QC on genotype calls |
| run.sample.qc | Perform basic sample-wise QC on genotype calls and... |
| samples.genotypes | Get sample metadata for a 'genotypes' object |
| scale_fill_heatmap | A red-to-orange color scale for heatmaps |
| scale_x_genome | Custom x-axis scale for genome coordinates. |
| scale_y_logp | Custom y-axis scale for -log10(p-values) |
| segregating | Identify segregating sites among a group of samples |
| sex.genotypes | Extract vector of sample sexes |
| sextable | Print summary table of sample sexes |
| sexysum | Summary stats for the sex chromosomes |
| sub-.genotypes | Indexing into a 'genotypes' object |
| subset.genotypes | Subset a 'genotypes' object by markers or samples |
| summarize.calls | Summarize genotype calls by sample or marker |
| summarize.filters | Show tally of filters failed by sites, samples. |
| summarize.intensity | Summarize hybridization intensity by sample |
| tdt.plink | Perform family-based transmission diseqiulibrium test (TDT)... |
| theme_axesonly | A graphics theme with only an x-axis |
| theme_gbrowse | A genome-browser like graphics theme |
| theme_heatmap | A graphics theme suitable for heatmaps |
| theme_nothing | A very minimal graphics theme |
| thin.genotypes | Thin markers to a specified density on the genetic map |
| tQN | Perform tQN normalization of intensity data. |
| twoway | Get two-way (marker x marker)-phenotype association |
| twoway.plot | Make graphical representation of a 'one-way'... |
| validate.genotypes | Check the integrity of a 'genotypes' object |
| weir.fst.plink | Compute Weir & Cockerham's F_st estimator using PLINK |
| write.hgdp | Export genotypes in Stanford HGDP format |
| write.plink | Write a 'genotypes' object as a PLINK binary fileset |
| xchrom | Shortcut for grabbing just chrX |
| ychrom | Shortcut for grabbing just chrY |
