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Protocols

LDheatmap specifications

Information


Unique identifier OMICS_19088
Name LDheatmap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.99-5
Stability Stable
Requirements
grid, IRanges, GenomicRanges, GenomeInfoDb, rtracklayer, lattice, ggplot2, snpStats, R(≥2.14.0), genetics
Maintained Yes

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Maintainers


  • person_outline Brad McNeney
  • person_outline Ji-Hyung Shin

Publication for LDheatmap

LDheatmap citations

 (69)
library_books

Hidden Effects of Seed Quality Breeding on Germination in Oilseed Rape (Brassica napus L.)

2018
Front Plant Sci
PMCID: 5891602
PMID: 29666629
DOI: 10.3389/fpls.2018.00419

[…] were taken into account which exceeded a value of -log10(p-value) = 2.1. local ld decay was calculated as coefficient of correlation (r2) between the single snp marker and visualized with r package ldheatmap (). for physical localization of snp markers, flanking sequences were blasted onto the b. napus darmor-bzh reference genome sequence assembly (version 4.1; ). snps were blasted using […]

library_books

Genome Wide Association Study for Identification and Validation of Novel SNP Markers for Sr6 Stem Rust Resistance Gene in Bread Wheat

2018
Front Plant Sci
PMCID: 5881291
PMID: 29636761
DOI: 10.3389/fpls.2018.00380

[…] sr6 ssr marker. linkage disequilibrium (r2) among the significant snps and the specific ssr marker located on the same chromosome was calculated by tassel 5.0 and visualized as a heatmap using ‘ldheatmap’ r package ()., haplotype block analysis was performed using haploview 4.2 software (). the snp data of the a-set was used to calculate the pair-wise ld between snps. a cutoff of 1% […]

library_books

ABCG2 contributes to the development of gout and hyperuricemia in a genome wide association study

2018
Sci Rep
PMCID: 5816657
PMID: 29453348
DOI: 10.1038/s41598-018-21425-7

[…] x, y and mitochondria chromosomes. a false discovery rate (fdr) was applied for analysis of further association with gout, and a linkage-disequilibrium (ld) test was drawn using the r program (ldheatmap). a one-way analysis of variance (anova) was applied to estimate the mean differences of demographic and biochemical data among those gout patients, hyperuricemia and controls. a logistic […]

library_books

Single‐nucleotide polymorphism discovery and panel characterization in the African forest elephant

2018
Ecol Evol
PMCID: 5817121
PMID: 29468037
DOI: 10.1002/ece3.3854

[…] the sequences to scaffolds and determine if the snps were located within a gene locus, and in particular within a coding region. pairwise linkage disequilibrium was tested for using the r package ldheatmap (default parameters) (shin, blay, mcneney, & graham, )., approximately one‐third of the samples yielded dna of sufficiently high‐molecular weight to attempt ddrad library preparation. […]

library_books

Integration of GWAS, pathway and network analyses reveals novel mechanistic insights into the synthesis of milk proteins in dairy cows

2018
Sci Rep
PMCID: 5766549
PMID: 29330500
DOI: 10.1038/s41598-017-18916-4

[…] region of cn loci on bta6 and the region of the β-lg gene (progestagen-associated endometrial protein, paep) on bta11 and their respective 1 mb flanking regions was calculated using the r package ldheatmap., pathway analyses were performed as detailed in dadousis et al. to identify the biological functions regulating the milk n fraction profile. briefly, the snps (nominal p-values < 0.05) […]

library_books

CRP Genotypes Predict Increased Risk to Co Present with Low Vitamin D and Elevated CRP in a Group of Healthy Black South African Women

2018
PMCID: 5800210
PMID: 29320465
DOI: 10.3390/ijerph15010111

[…] the akaike information criterion (aic). adherence to hardy–weinberg equilibrium (hwe) was tested by a chi-squared (χ2) test using snpassoc, and linkage disequilibrium (ld) was calculated using the ldheatmap library of the r package., variables identified in regression analyses were evaluated for co-linearity. possible environment–snps interaction was determined using snpassoc [] […]


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LDheatmap institution(s)
Department of Statistics & Actuarial Science, Simon Fraser University, Burnaby, BC, Canada
LDheatmap funding source(s)
Supported by Natural Sciences and Engineering Research Council of Canada grants 227972-00 and 213124-03, Juvenile Diabetes Research Foundation International grant 1-2001-873, Canadian Institutes of Health Research grants NPG-64869 and ATF-66667, and in part by the Mathematics of Information Technology and Complex Systems, Canadian National Centres of Excellence.

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