cgmisc: cgmisc: Enhanced Genome-wide Association Analyses and...

In cgmisc-team/cgmisc: Various functions useful in computational genetics, e.g. in GWAS

cgmisc: Enhanced Genome-wide Association Analyses and Visualisation.

Description

Package faciliating and enhancing data analyses and visualisation in genome-wide association studies. Contains functions for analyses of population structure, linkage structure, heterozygosity as well as wide range of data subsetting and manipulation.

Details

Package:	cgmisc
Version:	2.9.9
Date:	2015-04-28
Depends:	R (>= 3.0.1), GenABEL (>= 1.7.4), GenomicRanges (>= 1.18.4), rtracklayer (>= 1.26.2), ggplot2 (>= 1.0.1), grid (>= 3.1.1), wq (>= 0.4.3)
VignetteBuilder:	knitr
License:	GPL (>=2.10)

Index:

boxplot.snp	Box plot with genotypes
boxplot.snp.twoWay	SNP_box_twoWay
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	Scan for epistasis between a specified SNP and all others.
get.adjacent.markers	Get adjacent markers within a distance around the given marker.
get.chr.midpoints	Get middle point for each chromosome.
get.erv	Get endogenous retroviral sequences in canine genome,
get.overlap.windows	Get overlapping windows.
get.roh	Identify 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 format.
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 genomic region.
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 populations.
plot.qq	QQ plot with empirical p-values.
pop.allele.counts	Compare allele counts in two populations.

Author(s)

Marcin Kierczak <[e-mail]>
Jagoda Jablonska <[e-mail]>
Simon Forsberg <[e-mail]>
Veronika Scholz <[e-mail]>

Maintainer: Marcin Kierczak <[e-mail]>

References

Soon

See Also

GenABEL

cgmisc-team/cgmisc documentation built on Jan. 3, 2024, 9:52 p.m.