Package 'ReactomePA'

Datasets sample contains a sample of gene IDs.

Description

Datasets sample contains a sample of gene IDs.

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Pathway Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enriched pathways with FDR control.

Description

Pathway Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enriched pathways with FDR control.

Usage

enrichPathway(
  gene,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe = NULL,
  minGSSize = 10,
  maxGSSize = 500,
  qvalueCutoff = 0.2,
  organism = "human",
  readable = FALSE
)

Arguments

gene	a vector of entrez gene id.
pvalueCutoff	Cutoff value of pvalue.
pAdjustMethod	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
universe	background genes
minGSSize	minimal size of genes annotated by Ontology term for testing.
maxGSSize	maximal size of each geneSet for analyzing
qvalueCutoff	Cutoff value of qvalue
organism	one of "human", "rat", "mouse", "celegans", "yeast", "zebrafish", "fly".
readable	whether mapping gene ID to gene Name

Value

A enrichResult instance.

Author(s)

Guangchuang Yu http://ygc.name

See Also

enrichResult-class

Examples

gene <- c("11171", "8243", "112464", "2194",
			"9318", "79026", "1654", "65003",
			"6240", "3476", "6238", "3836",
			"4176", "1017", "249")
	yy = enrichPathway(gene, pvalueCutoff=0.05)
	head(summary(yy))
	#plot(yy)

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getALLEG

Description

get all entrezgene ID of a specific organism

Usage

getALLEG(organism)

Arguments

organism

species

Value

entrez gene ID vector

Author(s)

Yu Guangchuang

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getDb

Description

mapping organism name to annotationDb package name

Usage

getDb(organism)

Arguments

organism

one of supported organism

Value

annotationDb name

Author(s)

Yu Guangchuang

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gsePathway

Description

Gene Set Enrichment Analysis of Reactome Pathway

Usage

gsePathway(
  geneList,
  organism = "human",
  exponent = 1,
  minGSSize = 10,
  maxGSSize = 500,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  verbose = TRUE,
  nPerm = 1000,
  method = "multilevel",
  adaptive = FALSE,
  minPerm = 101,
  maxPerm = 1e+05,
  pvalThreshold = 0.1
)

Arguments

geneList	order ranked geneList
organism	organism
exponent	weight of each step
minGSSize	minimal size of each geneSet for analyzing
maxGSSize	maximal size of each geneSet for analyzing
pvalueCutoff	pvalue Cutoff
pAdjustMethod	pvalue adjustment method
verbose	print message or not
nPerm	The number of permutations for the "permute" method
method	one of "sample", "permute", "multilevel"
adaptive	logical
minPerm	minimal number of permutations for the "multilevel" method
maxPerm	maximal number of permutations for the "multilevel" method
pvalThreshold	The p-value threshold for the "multilevel" method

Value

gseaResult object

Author(s)

Yu Guangchuang

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gson_Reactome

Description

download the latest version of Reactome and stored in a 'GSON' object

Usage

gson_Reactome(organism = "human")

Arguments

organism

one of "human", "rat", "mouse", "celegans", "yeast", "zebrafish", "fly".

Value

a 'GSON' object

Examples

## Not run: 
rec_gson <- gson_Reactome("human")

## End(Not run)

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viewPathway

Description

view reactome pathway

Usage

viewPathway(
  pathName,
  organism = "human",
  readable = TRUE,
  foldChange = NULL,
  keyType = "ENTREZID",
  layout = "kk"
)

Arguments

pathName	pathway Name
organism	supported organism
readable	logical
foldChange	fold change
keyType	keyType of gene ID (i.e. names of foldChange, if available)
layout	graph layout

Details

plotting reactome pathway

Value

plot

Author(s)

Yu Guangchuang

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