Gwaspoly package
WebFeb 1, 2024 · GWASpoly.K-class: S4 class with genotypes, phenotypes, and polygenic covariance; GWASpoly.thresh-class: S4 class with results from genome-wide scan and detection... Keff: Effective number of markers; LD.plot: Plot LD vs distance; manhattan.plot: Create Manhattan plot; qq.plot: Quantile-Quantile (QQ) Plot; read.GWASpoly: Read in … WebThe function `GWASpoly` (same name as the package) conducts the hypothesis tests for each marker. The traditional GWAS model assumes an additive relationship between …
Gwaspoly package
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WebDec 17, 2024 · The R package GWASpoly for tetrapolyploids (Rosyara et al. 2016) was used to conduct the GWAS analysis on the panel. Principal component analysis was … WebGWAS was conducted using GWASpoly with Infinium Illumina 22 K V3 Potato Array. Significantly associated SNPs with external defect traits were located on chromosomes 3, 4, 6, and 7 while those with internal defect traits were located on chromosomes 3 and 10. The identified genomic regions may be important to improve heat tolerance in potatoes.
WebThe R package GWASpoly for tetrapolyploids (Rosyara et al. 2016) was used to conduct the GWAS analysis on the panel. Principal component analysis was used to estimate the population stratification using prcomp algorithm (www.r-project.org). The top four principal components were used to build up the P matrix for population structure correction. WebApr 14, 2024 · Quantitative trait locus (QTL) mapping was performed by genome-wide association for each trait BLUP using the full set of 18,493 markers with the GWASpoly package (Rosyara et al., 2016) in R analysis software. Meta-analysis was performed for trait BLUPs across all trials as well as individually for each of the two main trials.
WebFeb 4, 2015 · GWASpoly: R package for GWAS in autopolyploids Many of software packages are now available for performing GWAS in diploids however software … WebMar 20, 2024 · GWASpoly is tailored for autopolyploids via the Q + K mixed model and could model gene actions for polyploids (Rosyara et al., 2016). Six models were used for GWAS by GWASpoly, including a general …
WebJul 24, 2024 · To correct for population structure, PCA analysis was computed internally using the GWASpoly package and the four principal components were further used in GWAS analyses. Eight gene action models were tested for the tetraploid genotype calling: general, additive, simplex dominant alternative (simplex-dom-alt), simplex dominant …
WebGWAS was conducted using GWASpoly with Infinium Illumina 22 K V3 Potato Array. Significantly associated SNPs with external defect traits were located on chromosomes … if true in jsWebIn addition, GWASpoly package detected significant phenotype-genotype associations at the same region as GEMMA (Figures 4A,D), though the most significant variant locus detected by an additive ... if true in matlabWebFeb 23, 2024 · Case-control genome-wide association studies (GWAS) with SolCAP SNP array data for chip-processing clones versus all other market classes in the 393-line potato diversity panel were performed using the GWASpoly R package, enabling detection of significant signals on chromosome 10. if true change cell color google sheetsWebWe therefore developed and released the R package GWASpoly, which is available on the PD's website (potatobreeding.cals.wisc.edu/software) and is already being used by several other research groups. Objective 2. Identify genomic regions for marker-assisted selection through GWAS of agronomic and processing traits, such as reducing sugars ... if true then the output is pretty printedWebThe function GWASpoly (same name as the package) conducts the hypothesis tests for each marker. The traditional GWAS model assumes an additive relationship between … if true highlight rowif true in bashWebIt is a complete ready-to-use software package (Linux operating system, R system and libraries, file manager, html browser, and MultiGWAS application). The entire system consists of a single archive file that corresponds to a virtual appliance (also known as a virtual machine). ... "gwaspoly" format: table with comma separated values (.csv ... if true statements python