View source: R/vis_functionalSites.R
siteEFF | R Documentation |
Calculation of Sites Effective
siteEFF(hap, pheno, phenoNames, quality = FALSE, method = "auto",
p.adj = "none")
hap |
object of "hapResult" class |
pheno |
phenotype data, with column names as pheno name and row name as accessions. |
phenoNames |
pheno names used for analysis, if missing,
will use all pheno names in |
quality |
bool type, indicate whther the type of phenos are quality or
quantitative. Length of |
method |
character or character vector with length equal with
|
p.adj |
character, indicate correction method. Could be "BH", "BY", "none" |
The site EFF was determinate by the phenotype difference between each site geno-type.
The p was calculated with statistical analysis method as designated by the
parameter method
. If method
set as "auto", then
chi.test will be
selected for quantity phenotype, eg.: color;
for quantity phynotype, eg.: height, with at least 30 observations per
geno-type and fit Gaussian distribution t.test will be performed, otherwise
wilcox.test will be performed.
a list containing two matrix names as "p" and "EFF", with column name are pheno names and row name are site position. The matrix names as "p" contains all p-value. The matrix named as "EFF" contains scaled difference between each geno-types per site.
data("geneHapR_test")
# calculate site functional effect
# siteEFF <- siteEFF(hapResult, pheno, names(pheno))
# plotEFF(siteEFF, gff = gff, Chr = "scaffold_1")
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