API for andrewparkermorgan/argyle
Basic interface and QC for genotypes from Illumina Infinium arrays
| Global functions | |
|---|---|
| $.genotypes | Man page |
| [.genotypes | Man page |
| apply.filters | Man page |
| argyle | Man page |
| argyle-package | Man page |
| as.data.frame.genotypes | Man page |
| as.genotypes | Man page |
| as.rqtl | Man page |
| assoc.plink | Man page |
| autosomes | Man page |
| bafplot | Man page |
| blank.grob | Man page |
| cbind.genotypes | Man page |
| consensus | Man page |
| dist.genotypes | Man page |
| dotplot | Man page |
| dotplot.genotypes | Man page |
| drop.intensity | Man page |
| ex | Man page |
| export.doqtl | Man page |
| filter.plink | Man page |
| filters | Man page |
| filters.genotypes | Man page |
| fix.strand.swaps | Man page |
| fixed.diffs | Man page |
| freq | Man page |
| freqplot | Man page |
| genoapply | Man page |
| genotypes | Man page |
| get.baf | Man page |
| get.call | Man page |
| get.intensity | Man page |
| ggmanhattan | Man page |
| guess.parents | Man page |
| has.intensity | Man page |
| head | Man page |
| head.genotypes | Man page |
| heatmap | Man page |
| heatmap.genotypes | Man page |
| heterozygosity | Man page |
| informative | Man page |
| intensity | Man page |
| intensity.genotypes | Man page |
| intensity.vs.ref | Man page |
| intensityhist | Man page |
| is.filtered | Man page |
| kinship.plink | Man page |
| ld.plink | Man page |
| maf | Man page |
| markers | Man page |
| markers.genotypes | Man page |
| mds.plink | Man page |
| mendel.distance | Man page |
| merge.genotypes | Man page |
| missingness | Man page |
| nmiss | Man page |
| oneway | Man page |
| oneway.plot | Man page |
| pca | Man page |
| pca.genotypes | Man page |
| pca.plink | Man page |
| plinkify | Man page |
| plot.clusters | Man page |
| plot.haplotypes | Man page |
| plot.pca.result | Man page |
| predict.f1 | Man page |
| predict.haplogroup | Man page |
| predict.sex | Man page |
| prop.het | Man page |
| prune.plink | Man page |
| qcplot | Man page |
| quantile.normalize | Man page |
| rbind.genotypes | Man page |
| read.beadstudio | Man page |
| read.plink | Man page |
| recode | Man page |
| recode.genotypes | Man page |
| recode.to.parent | Man page |
| reconstruct.haps | Man page |
| replace.map | Man page |
| replace.names | Man page |
| run.marker.qc | Man page |
| run.sample.qc | Man page |
| samples | Man page |
| samples.genotypes | Man page |
| scale_fill_heatmap | Man page |
| scale_x_genome | Man page |
| scale_y_logp | Man page |
| segregating | Man page |
| sex.genotypes | Man page |
| sextable | Man page |
| sexysum | Man page |
| subset.genotypes | Man page |
| summarize.calls | Man page |
| summarize.filters | Man page |
| summarize.intensity | Man page |
| tQN | Man page |
| tdt.plink | Man page |
| theme_axesonly | Man page |
| theme_gbrowse | Man page |
| theme_heatmap | Man page |
| theme_nothing | Man page |
| thin | Man page |
| thin.genotypes | Man page |
| twoway | Man page |
| twoway.plot | Man page |
| validate | Man page |
| validate.genotypes | Man page |
| weir.fst | Man page |
| weir.fst.plink | Man page |
| write.hgdp | Man page |
| write.plink | Man page |
| xchrom | Man page |
| ychrom | Man page |
