genotypeSummary {GeneticsBase} | R Documentation |
print the summary of genotypes sorted by markers
genotypeSummary(object, by = NULL, confidence = 0.95, alpha = 1 - confidence, show = TRUE, HWE.method = c("simulate", "exact"), simulate.p.value = TRUE, B = 10000, verbose = FALSE, includeOverall = FALSE, omitRepeats = TRUE, founderOnly = FALSE, ...)
object |
geneSet object |
by |
optional column name, by which the summary is desired. Default is NULL. |
confidence |
confidence intervals of Genotype frequencies within each marker (default is 95%) |
alpha |
Type -1 error rate = (1- confidence) |
show |
No longer used |
HWE.method |
Method to be used for Hardy-Weinberg Equilibrium Significance Test, exact or simulate |
simulate.p.value |
No longer used |
B |
No longer used |
verbose |
No longer used |
includeOverall |
logical value (TRUE/FALSE) indicating whether overall summary is also needed, default = FALSE |
omitRepeats |
logical value (TRUE/FALSE) indicating whether Gene name and marker name should be printed repeatedly for each Genotype, default = TRUE |
founderOnly |
logical value (TRUE/FALSE) indicating whether founder information should be extracted from the geneSet object, default = FALSE |
... |
any further arguments to print |
We can print the genotypeSummary on screen, or save in .html format or .tex format
Nitin Jain nitin.jain@pfizer.com
library(GeneticsBase) data(CAMP) temp <- genotypeSummary(CAMP) print(temp) txt(temp, filename="genotypeSummary.txt") html(temp, filename="genotypeSummary.html") latex(temp, filename="genotypeSummary.tex")