LDheatmap protocols

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LDheatmap specifications

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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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  • person_outline Brad McNeney <>
  • person_outline Ji-Hyung Shin <>

Publication for LDheatmap

LDheatmap in pipelines

 (4)
2017
PMCID: 5540500
PMID: 28764648
DOI: 10.1186/s12870-017-1080-9

[…] using clustalx version 2.1 []. polymorphisms were confirmed by visual inspection. linkage disequilibrium among polymorphisms was calculated and plotted in r using the ‘genetics’ (ver 1.3.8.1) and ‘ldheatmap’ packages (ver 0.99–1) []. for the nucleotide polymorphisms associated with cld variation and which would generate amino acid substitutions, estimation of the likelihood that a variant […]

2016
PMCID: 4817125
PMID: 27033636
DOI: 10.1038/srep23805

[…] set as 0.01/total snps. the total snps used for calculating significance threshold in the first and second association tests were 15 and 135, respectively. the ld plots of snps were drawn using the ldheatmap package., the coding sequence of the seven genes, which were randomly chosen to verify the negative regulations computed for resistance related gene homologs by qrt-pcr (), was downloaded […]

2016
PMCID: 5073211
PMID: 27818672
DOI: 10.3389/fpls.2016.01576

[…] for the relative phenotypic values were performed using r software., linkage disequilibrium (ld) blocks containing snp loci associated with target traits were generated using the r software package “ldheatmap” (shin et al., ). ld blocks harboring significantly associated snps were then defined as the candidate genome regions. the genes distributed in these regions were collected. the gene […]

2011
PMCID: 3287149
PMID: 22133426
DOI: 10.1186/2041-2223-2-24

[…] [,]. the four-gamete rule was computed for each pair of loci in each gene. a value of 1 was assigned when the four-gamete rule could not be rejected and 0 when it could. ldheatmap http://stat-db.stat.sfu.ca:8080/statgen/research/ldheatmap/[] was used to plot the matrix of loci for each gene. measures of genetic diversity, including nucleotide diversity (π) [] […]

LDheatmap in publications

 (67)
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 […]

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% […]

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 […]

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. […]

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) […]

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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