vGWASparallel: Variance Genome-wide Association (parallel)

In kullrich/vGWAS: Variance Heterogeneity Genome-wide Association Study - Reimplementation

Variance Genome-wide Association (parallel)

Description

Variance Genome-wide association for using nonparametric variance test and other

Usage

vGWASparallel(phenotype, geno.matrix, marker.map = NULL,
chr.index = NULL, geno.snp = "row", method = "bfmedian", test.alpha = 0.05,
test.na.rm = TRUE, p.adjust.method = "none", include.het = FALSE, pB = TRUE,
ncores = 1)

Arguments

phenotype	a numeric or logical vector of the phenotyic values.
geno.matrix	a matrix or data.frame or sparseMatrix with individuals as columns and markers as rows (geno.snp = "row") or individuals as rows and markers as columns (geno.snp = "col").
marker.map	a numeric vector giving the marker map positions for each chromosome.
chr.index	a numeric vector giving the chromosome index for each marker.
geno.snp	if individuals at columns and markers at rows use "row" else if individuals at rows and markers at columns use "col"
method	the test method to use (default = bfmedian). Default is set to the Brown-Forsythe's Test of Equality of Variances using group medians. There are 31 other tests available via the onewaytests package: Alvandi's F test ("af"), Alexander-Govern test ("ag"), Alvandi's generalized p-value ("agp"), One-way analysis of variance ("aov"), Approximate F test ("ap"), Adjusted Welch's heteroscedastic F test ("aw"), B square test ("b2"), Brown-Forsythe test ("bf"), Box F test ("box"), Cochran test ("cochran"), Generalized tests equivalent to Parametric Bootstrap ("gtb"), Generalized tests equivalent to Fiducial tests ("gtf"), Variance homogeneity tests ("homog"), James second order test ("james"), Johansen F test ("johansen"), Kruskal-Wallis test ("kw"), Modified Brown-Forsythe test ("mbf"), Mann-Whitney U test ("mw"), Anderson-Darling normility test ("nor_ad"), Cramer-vin Mises normility test ("nor_cvm"), Kolmogorov-Smirnov normility test ("nor_ks"), Pearson Chi-square normility test ("nor_pct"), Shapiro-Wilk normility test ("nor_sw"), Shapiro-Francia normility test ("nor_sf"), Permutation F test ("pf"), Scott-Smith test ("ss"), Student's t-test ("st"), Welch-Aspin test ("wa"), Welch's heteroscedastic F test with trimmed means and Winsorized variances ("welch"), Weerahandi's generalized F test ("wgf"), Welch's t-test ("wt").
test.alpha	the level of significance to assess the statistical difference. Default is set to alpha = 0.05.
test.na.rm	a logical value indicating whether NA values should be stripped before the computation proceeds. Default us set to TRUE.
p.adjust.method	correction method (default = "none"). There are 8 p-value correction methods available via the p.adjust function: "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
include.het	specify if heterozygous calls should be split and added equally to homozygous ref and alt counts (default = FALSE)
pB	show progress bar
ncores	number of cores to parallelize (default = 1)

Value

a data.frame containing columns of marker names, chromosome indices, marker.map positions, test statistic values, and p.value for each position.

Author(s)

Xia Shen

Kristian Ullrich

References

Shen, X., Pettersson, M., Ronnegard, L. and Carlborg, O. (2011): Inheritance beyond plain heritability: variance-controlling genes in Arabidopsis thaliana. PLoS Genetics, 8, e1002839.

Ronnegard, L., Shen, X. and Alam, M. (2010): hglm: A Package for Fitting Hierarchical Generalized Linear Models. The R Journal, 2(2), 20-28.

See Also

package-vGWAS onewaytests

Examples

# ----- load data ----- #
data(pheno)
data(geno)
data(chr)
data(map)
# ----- variance GWA scan ----- #
vgwa <- vGWASparallel(phenotype = pheno, geno.matrix = geno,
marker.map = map, chr.index = chr,
geno.snp = "col", pB = FALSE)
# ----- other test GWA scan ----- #
vgwa.mw <- vGWASparallel(phenotype = pheno, geno.matrix = geno,
marker.map = map, chr.index = chr,
geno.snp = "col", method = "mw", pB = FALSE)
# ----- multiple cores ----- #
vgwa.st <- vGWASparallel(phenotype = pheno, geno.matrix = geno,
marker.map = map, chr.index = chr,
geno.snp = "col", method = "st", ncores = 2, pB = FALSE)

kullrich/vGWAS documentation built on June 10, 2025, 3:56 a.m.