Usage
dEnricher(data, identity = c("symbol", "entrez"),
check.symbol.identity = FALSE, genome = c("Hs", "Mm", "Rn", "Gg", "Ce",
"Dm", "Da", "At"), ontology = c("GOBP", "GOMF", "GOCC", "PS", "DO",
"HPPA",
"HPMI", "HPON", "MP", "MsigdbC1", "MsigdbC2CGP", "MsigdbC2CP",
"MsigdbC2KEGG",
"MsigdbC2REACTOME", "MsigdbC2BIOCARTA", "MsigdbC3TFT", "MsigdbC3MIR",
"MsigdbC4CGN", "MsigdbC4CM", "MsigdbC5BP", "MsigdbC5MF", "MsigdbC5CC",
"MsigdbC6", "MsigdbC7"), sizeRange = c(10, 1000), which_distance =
NULL,
test = c("FisherTest", "HypergeoTest", "BinomialTest"),
p.adjust.method = c("BH", "BY", "bonferroni", "holm", "hochberg",
"hommel"),
ontology.algorithm = c("none", "pc", "elim", "lea"), elim.pvalue =
0.01,
lea.depth = 2, verbose = T,
RData.location = "http://dnet.r-forge.r-project.org/data")Arguments
data
an input vector. It contains either Entrez
Gene ID or Symbol
identity
the type of gene identity (i.e. row names
of input data), either "symbol" for gene symbols (by
default) or "entrez" for Entrez Gene ID. The option
"symbol" is preferred as it is relatively stable from one
update to another; also it is possible to search a
check.symbol.identity
logical to indicate whether
synonyms will be searched against when gene symbols
cannot be matched. By default, it sets to FALSE since it
may take a while to do such check using all possible
synoyms
genome
the genome identity. It can be one of "Hs"
for human, "Mm" for mouse, "Rn" for rat, "Gg" for
chicken, "Ce" for c.elegans, "Dm" for fruitfly, "Da" for
zebrafish, and "At" for arabidopsis
ontology
the ontology supported currently. It can
be "GOBP" for Gene Ontology Biological Process, "GOMF"
for Gene Ontology Molecular Function, "GOCC" for Gene
Ontology Cellular Component, "PS" for phylostratific age
information, "DO" for Disease Ontology, "HPPA" f
sizeRange
the minimum and maximum size of members
of each gene set in consideration. By default, it sets to
a minimum of 10 but no more than 1000
which_distance
which distance of terms in the
ontology is used to restrict terms in consideration. By
default, it sets to 'NULL' to consider all distances
test
the statistic test used. It can be
"FisherTest" for using fisher's exact test,
"HypergeoTest" for using hypergeometric test, or
"BinomialTest" for using binomial test. Fisher's exact
test is to test the independence between gene group
(genes belonging to
p.adjust.method
the method used to adjust
p-values. It can be one of "BH", "BY", "bonferroni",
"holm", "hochberg" and "hommel". The first two methods
"BH" (widely used) and "BY" control the false discovery
rate (FDR: the expected proportion of false discoveries
amongst t
ontology.algorithm
the algorithm used to account
for the hierarchy of the ontology. It can be one of
"none", "pc", "elim" and "lea". For details, please see
'Note'
elim.pvalue
the parameter only used when
"ontology.algorithm" is "elim". It is used to control how
to declare a signficantly enriched term (and subsequently
all genes in this term are eliminated from all its
ancestors)
lea.depth
the parameter only used when
"ontology.algorithm" is "lea". It is used to control how
many maximum depth is uded to consider the children of a
term (and subsequently all genes in these children term
are eliminated from the use for the recalculation of the
verbose
logical to indicate whether the messages
will be displayed in the screen. By default, it sets to
false for no display
RData.location
the characters to tell the location
of built-in RData files. By default, it remotely locates
at "http://dnet.r-forge.r-project.org/data". For
the user equipped with fast internet connection, this
option can be just left as default. But it is al