Stat.nonpara: U test (non parameter test) for permutation. This is one...

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

U test (non parameter test) for permutation. This is one probe vs nearby gene which is good for computing each probes for nearby genes.

Usage

Stat.nonpara(
  Probe,
  NearGenes,
  Top = NULL,
  correlation = "negative",
  unmethy = NULL,
  methy = NULL,
  Meths = Meths,
  Exps = Exps
)

Arguments

Probe	A character of name of Probe in array.
NearGenes	A list of nearby gene for each probe which is output of GetNearGenes function.
Top	A number determines the percentage of top methylated/unmethylated samples. Only used if unmethy and methy are not set.
correlation	Type of correlation to evaluate (negative or positive). Negative (default) checks if hypomethylated region has a upregulated target gene. Positive checks if region hypermethylated has a upregulated target gene.
unmethy	Index of U (unmethylated) group.
methy	Index of M (methylated) group.
Meths	A matrix contains methylation for each probe (row) and each sample (column).
Exps	A matrix contains Expression for each gene (row) and each sample (column).

Value

U test results

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.