Man pages for cgmisc-team/cgmisc
Various functions useful in computational genetics, e.g. in GWAS.

bigRR.dataThe 'bigRR.data' class This class contains results of running...
boxplot.snpBox plot with genotypes
boxplot.snp.twoWaySNP_box_twoWay
cgmisccgmisc: Enhanced Genome-wide Association Analyses and...
choose.top.snpsSelect the highest r2 SNPs to a given top marker.
chr.x.fix.canfamFix canine X chromosome naming
clump.markersClump markers according to their LD.
compute.fstatsCompute Fst fixation index for two populations
create.haploview.infoPrepare a PHASE input file from gwaa data
epistasis.scanepistasisScan
fstats.resultThe 'fstats.result' class This class contains results...
get.adjacent.markersGet adjacent markers within a distance around the given...
get.chr.midpointsGet middle point for each chromosome
get.ervGet endogenous retroviral sequences in canine genome
get.ld.colorsPlot results of 'get.LD.colors'
get.overlap.windowsGet overlapping windows
get.rohRuns of homozygosity
gwaa.to.bedCreate a BED file with GWAS p-values in a region
gwaa.to.bigrrConverts gwaa-data-class GenABEL object to a bigRR-readable...
gwaa.to.phasePrepare a PHASE input file from gwaa data.
gwaa.to.vgwasConvert GenABEL data structure to vGWAS data structure
het.overlap.windCalculates heterozygosity for windows
open.region.ucscOpen UCSC GenomeBrowser for selected region
pac.resultThe 'pac.result' class This class contains results of running...
phase.to.fastaConverts haplotypes from PHASE output to FASTA format.
phase.to.haploviewConverts PHASE output to HaploView readable format.
plot.clumpsPlot marker clumps on Manhattan plot.
plot.ervPlot endogenous retroviral sequences in canine genome.
plot.fstatsPlot results of 'compute.fstats'
plot.genesPlot genes provided in a bed file
plot.ld.decayPlots LD decay pattern for a given data
plot.manhattan.genesPlot LD pattern and MAF in a Manhattan plot
plot.manhattan.ldPlot LD pattern and MAF in a Manhattan plot
plot.overlapPlots average heterozygosities for overlapping windows
plot.pacPlot p-values of allele count differences between...
plot.qqQQ plot with empirical p-values
pop.allele.countsCompare allele counts in two populations.
cgmisc-team/cgmisc documentation built on May 12, 2017, 1:18 a.m.