hyperGeoTest: Perform hypergeometric test

In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

Perform hypergeometric test

Description

Perform hypergeometric test

Usage

hyperGeoTest(
  row.group,
  col.group,
  row.prefix = "",
  col.prefix = "",
  lower.tail = FALSE,
  title = "",
  log10.lowest = 5,
  print.fig = TRUE,
  adjusted.p = NULL,
  remove.na = FALSE,
  bar.color = "npg",
  chiq.square.test = T,
  not.consider = NA,
  top.piont.color = "#0269A4"
)

Arguments

lower.tail	Default FALSE
log10.lowest	Default 3. Minimux or maximum log10 value. Useful when meet inf or draw heatmap
print.fig	Default print the figure
adjusted.p	If to adjust P value c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")
remove.na	If to remove NA
bar.color	palatte for barplot
not.consider	A vector that not consider the inside element
top.piont.color	Default "#0269A4"

Value

list(barplot, pval.df.log, pval.df, plot)

Examples

g1 = sample(c("G1","G2","G3"),10, replace = T)
g2 = sample(c("1","2","3"),10, replace = T)
loonR::hyperGeoTest(g1, g2, col.prefix = "E")

ProfessionalFarmer/loonR documentation built on Oct. 9, 2024, 9:56 p.m.