bigRR.data | The 'bigRR.data' class This class contains results of running... |
boxplot.snp | Box plot with genotypes |
boxplot.snp.twoWay | SNP_box_twoWay |
cgmisc | cgmisc: Enhanced Genome-wide Association Analyses and... |
choose.top.snps | Select the highest r2 SNPs to a given top marker. |
chr.x.fix.canfam | Fix canine X chromosome naming |
clump.markers | Clump markers according to their LD. |
compute.fstats | Compute Fst fixation index for two populations |
create.haploview.info | Prepare a PHASE input file from gwaa data |
epistasis.scan | epistasisScan |
fstats.result | The 'fstats.result' class This class contains results... |
get.adjacent.markers | Get adjacent markers within a distance around the given... |
get.chr.midpoints | Get middle point for each chromosome |
get.erv | Get endogenous retroviral sequences in canine genome |
get.ld.colors | Plot results of 'get.LD.colors' |
get.overlap.windows | Get overlapping windows |
get.roh | Runs of homozygosity |
gwaa.to.bed | Create a BED file with GWAS p-values in a region |
gwaa.to.bigrr | Converts gwaa-data-class GenABEL object to a bigRR-readable... |
gwaa.to.phase | Prepare a PHASE input file from gwaa data. |
gwaa.to.vgwas | Convert GenABEL data structure to vGWAS data structure |
het.overlap.wind | Calculates heterozygosity for windows |
open.region.ucsc | Open UCSC GenomeBrowser for selected region |
pac.result | The 'pac.result' class This class contains results of running... |
phase.to.fasta | Converts haplotypes from PHASE output to FASTA format. |
phase.to.haploview | Converts PHASE output to HaploView readable format. |
plot.clumps | Plot marker clumps on Manhattan plot. |
plot.erv | Plot endogenous retroviral sequences in canine genome. |
plot.fstats | Plot results of 'compute.fstats' |
plot.genes | Plot genes provided in a bed file |
plot.ld.decay | Plots LD decay pattern for a given data |
plot.manhattan.genes | Plot LD pattern and MAF in a Manhattan plot |
plot.manhattan.ld | Plot LD pattern and MAF in a Manhattan plot |
plot.overlap | Plots average heterozygosities for overlapping windows |
plot.pac | Plot p-values of allele count differences between... |
plot.qq | QQ plot with empirical p-values |
pop.allele.counts | Compare allele counts in two populations. |
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