RandomComparePheno: RandomComparePheno

In alexcis95/PhenoExam: Compare the likeness of phenotypes terms between groups of genes

RandomComparePheno

Description

This function measures statistically significant phenotype similarities between gene sets and detects significant differential phenotypes for them.

Usage

RandomComparePheno(
  geneset,
  genesetcompare,
  organism = "human",
  database = "HPO",
  p.value = 0.05,
  nulltestnumber = 100,
  seed = 1,
  conditional_case = F,
  url = F,
  linux = T,
  adjust = "bonferroni",
  POR = "jaccard"
)

Arguments

geneset	A vector with genes symbol.
genesetcompare	A vector with gene symbol.
organism	A string parameter: "human" if you have human genes and "mouse" if you have mouse genes
database	A string parameter with different options. You can define a vector with the databases.
p.value	Cut of p value as they are relevant terms
nulltestnumber	A number of random genes subset.
seed	A seed.
url	A logical parameter. T if you want interactive links
linux	A logical parameter. T if you use linux SO, this is the default option
adjust	A string parameter. You have two options: "bonferroni" is the default option and you can choose "fdr" for False Discovery Rate.
POR	A string parameter. You have two options: Use the Jaccard index "jaccard" is the default option and you can choose the Forbes coefficient "forbes".

Details

This function has developed by Alejandro Cisterna García as part of his PhD mentored by Juan Antonio Botía Blaya

alexcis95/PhenoExam documentation built on Jan. 6, 2023, 1:34 p.m.