EnrichDO (version 0.1-1)

doEnrich: doEnrich

Description

given a list of genes, this function combines topological properties of the disease ontology structure for enrichment analysis.

Usage

doEnrich(
  interestGenes,
  test = c("hypergeomTest", "fisherTest", "binomTest", "chisqTest", "logoddTest"),
  method = c("BH", "holm", "hochberg", "hommel", "bonferroni", "BY", "fdr", "none"),
  m = 1,
  maxGsize = 5000,
  minGsize = 5,
  traditional = FALSE,
  delta = 0.01,
  penalize = TRUE,
  allDOTerms = FALSE
)

Value

A EnrichResult instance.

Arguments

interestGenes

a vector of gene IDs.

test

One of 'fisherTest','hypergeomTest','binomTest','chisqTest' and 'logoddTest' statistical model. Default is hypergeomTest.

method

One of 'holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY','fdr' and 'none',for P value correction.

m

Set the maximum number of ancestor layers for ontology enrichment. Default is layer 1.

maxGsize

indicates that doterms with more annotation genes than maxGsize are ignored, and the P value of these doterms is set to 1.

minGsize

indicates that doterms with less annotation genes than minGsize are ignored, and the P value of these doterms is set to 1.

traditional

a logical variable, TRUE for traditional enrichment analysis, FALSE for enrichment analysis with weights. Default is FALSE.

delta

Set the threshold of nodes, if the p value of doterm is greater than delta, the nodes are not significant, and these nodes are not weighted.

penalize

Logical value, whether to add a penalty to the node.Adding a penalty will look for nodes with more branches.

allDOTerms

Logical value, whether to store all doterms in EnrichResult, defaults is FALSE (only significant nodes are retained).

Author

Haixiu Yang

Examples

#The enrichment results were obtained by using demo.data
demo.data <- c(1636,351,102,2932,3077,348,4137,54209)
demo_result <- doEnrich(interestGenes=demo.data,maxGsize = 100, minGsize=10)