Usage
dcAlgo(anno.file, architecture.file, output.file = NULL, ontology =
c(NA,
"GOBP", "GOMF", "GOCC", "DO", "HPPA", "HPMI", "HPON", "MP", "EC", "KW",
"UP"),
feature.mode = c("supra", "individual", "comb"), min.overlap = 3,
fdr.cutoff = 0.001, hscore.type = c("zscore", "fdr"), parallel = TRUE,
multicores = NULL, verbose = T, RData.ontology.customised = NULL,
RData.location =
"https://github.com/hfang-bristol/RDataCentre/blob/master/dcGOR")
Arguments
anno.file
an annotation file containing annotations between
proteins/genes and ontology terms. For example, a file containing
annotations between human genes and HP terms can be found in
http://dcgor.r-forge.r-project.org/data/Algo/HP_anno.txt. As seen
in this example, the input file must contain the header (in the first
row) and two columns: 1st column for 'SeqID' (actually these IDs can be
anything), 2nd column for 'termID' (HP terms). Note: the file should
use the tab delimiter as the field separator between columns architecture.file
an architecture file containing domain
architectures (including individual domains) for proteins/genes. For
example, a file containing human genes and domain architectures can be
found in
http://dcgor.r-forge.r-project.org/data/Algo/SCOP_architecture.txt.
As seen in this example, the input file must contain the header (in the
first row) and two columns: 1st column for 'SeqID' (actually these IDs
can be anything), 2nd column for 'Architecture' (SCOP domain
architectures, each represented as comma-separated domains). Note: the
file should use the tab delimiter as the field separator between
columns output.file
an output file containing results. If not NULL, a
tab-delimited text file will be also written out, with 1st column
'Feature_id' for features/domains, 2nd column 'Term_id' for ontology
terms, 3rd column 'Score' for hypergeometric scores (indicative of
strength for feature-term associations). Otherwise, there is no output
file (by default)
ontology
the ontology identity. It can be "GOBP" for Gene
Ontology Biological Process, "GOMF" for Gene Ontology Molecular
Function, "GOCC" for Gene Ontology Cellular Component, "DO" for Disease
Ontology, "HPPA" for Human Phenotype Phenotypic Abnormality, "HPMI" for
Human Phenotype Mode of Inheritance, "HPON" for Human Phenotype ONset
and clinical course, "MP" for Mammalian Phenotype, "EC" for Enzyme
Commission, "KW" for UniProtKB KeyWords, "UP" for UniProtKB UniPathway.
For details on the eligibility for pairs of input domain and ontology,
please refer to the online Documentations at
http://supfam.org/dcGOR/docs.html. If NA, then the user has to
input a customised RData-formatted file (see
RData.ontology.customised below) feature.mode
the mode of how to define the features thereof. It
can be: "supra" for combinations of one or two successive domains
(including individual domains; considering the order), "individual" for
individual domains only, and "comb" for all possible combinations
(including individual domains; ignoring the order)
min.overlap
the minimum number of overlaps with each term in
consideration. By default, it sets to a minimum of 3
fdr.cutoff
the fdr cutoff to call the significant associations
between features and terms. By default, it sets to 1e-3
hscore.type
the type of defining the hypergeometric score. It
can be: "zscore" for z-score (by default), "fdr" for fdr (after being
transformed via $-1*log_2(fdr)$)
parallel
logical to indicate whether parallel computation with
multicores is used. By default, it sets to true, but not necessarily
does so. Partly because parallel backends available will be
system-specific (now only Linux or Mac OS). Also, it will depend on
whether these two packages "foreach" and "doMC" have been installed. It
can be installed via:
source("http://bioconductor.org/biocLite.R");
biocLite(c("foreach","doMC")). If not yet installed, this option will
be disabled
multicores
an integer to specify how many cores will be
registered as the multicore parallel backend to the 'foreach' package.
If NULL, it will use a half of cores available in a user's computer.
This option only works when parallel computation is enabled
verbose
logical to indicate whether the messages will be
displayed in the screen. By default, it sets to TRUE for display
RData.ontology.customised
a file name for RData-formatted file
containing an object of S4 class 'Onto' (i.g. ontology). By default, it
is NULL. It is only needed when the user wants to perform customised
analysis using their own ontology. See dcBuildOnto for
how to creat this object RData.location
the characters to tell the location of built-in
RData files. See dcRDataLoader for details