fea_gtLinker {FGNet} | R Documentation |
Performs the functional enrichment analysis and clustering through Gene-Term Linker [1] (requires internet connection).
Since Gene-Term Linker takes a while to analyze the gene list, the process has been splitted in two steps:
fea_gtLinker(): Submits the query
fea_gtLinker_getResults(): Retrieves the results of the analysis. It might take a few minutes for the results to become available.
fea_gtLinker(geneList, organism = "Hs", annotations = c("GO_Biological_Process", "GO_Molecular_Function", "GO_Cellular_Component", "InterPro_Motifs"), minSupport = 4, serverWS = "http://gtlinker.cnb.csic.es:8182") fea_gtLinker_getResults(jobID = NULL, organism = NULL, jobName = NULL, alreadyDownloaded = FALSE, keepTrying = FALSE, serverWeb = "http://gtlinker.cnb.csic.es", serverWS = "http://gtlinker.cnb.csic.es:8182")
fea_gtLinker():
geneList |
character vector. List of genes to analyze. |
annotations |
character vector. Annotation spaces for the functional analysis. |
minSupport |
numeric. Minimum number of genes per group. |
common arguments:
serverWS |
character. GeneTerm Linker webservice server. |
organism |
character. "Hs" (Homo sapiens) or "Sc" (Saccharomyces cerevisiae). |
fea_gtLinker_getResults():
jobID |
numeric. ID of the job/analysis in GeneTerm Linker. |
jobName |
character. Folder name and prefix for the files. |
alreadyDownloaded |
logical. If the files have already been downloaded, these will be read instead of downloaded again. |
keepTrying |
logical. If true, if the job has not finished, it will keep trying to get the results every few seconds. |
serverWeb |
character. GeneTerm Linker web server. It should match the web service or web address in which the analysis was performed. |
fea_gtLinker() returns the jobID of the analysis
fea_gtLinker_getResults() returns an invisible list with the folowing fields:
queryArgs
list with the arguments for the query.
metagroups
data.frame containing the metagroups and their information:
Metagroup: Metagroup ID.
Size: Number of gene-term sets supporting the metagroup.
Diameter: Maximum Cosine distance within the GeneTerm-sets of each metagroup (ranges from 0 to 1).
Similarity: 1 - average Cosine distance within the GeneTerm-sets of each metagroup (ranges from 0 to 1). Distance and similarity calculations are done based on the genes present in the metagroups.
Silhouette Width: Measures the compactness and proximity of multiple groups (ranges from 1 to -1). Metagroups with negative Silhouette Width usually include diverse annotations and genes with low functional coherence.
Genes: Genes in the metagroup.
nGenes: Number of genes in the metagroup.
nref_list: Number of annotated genes in the reference list.
pValue: Adjusted p-value.
Terms: Non-generic terms in the metagroup.
geneTermSets
data.frame containing the gene-term sets that support each metagroup.
Metagroup: Id of the metagroup the gene-term set belongs to.
Genes: Genes in the gene-term set.
nGenes: Number of annotated genes in the input list. In brackets: Total number of genes in the input list.
nref_list: Number of annotated genes in the reference list. In brackets: Total number of genes in the reference list.
pValue: Adjusted p-value.
Terms: Terms in the gene-term set.
fileName
.txt file with the formatted FEA results.
[1] Fontanillo C, Nogales-Cadenas R, Pascual-Montano A, De Las Rivas J (2011) Functional Analysis beyond Enrichment: Non-Redundant Reciprocal Linkage of Genes and Biological Terms. PLoS ONE 6(9): e24289. URL: http://gtlinker.cnb.csic.es
Other FEA tools:
fea_david()
(Requires internet connection)
To import results from a previous/external FEA analysis: format_david()
, format_results()
and readGeneTermSets()
.
Overview of the package: FGNet
Package tutorial: vignette("FGNet-vignette")
## Not run: ### Execute FEA: genesYeast <- c("ADA2", "APC1", "APC11", "APC2", "APC4", "APC5", "APC9", "CDC16", "CDC23", "CDC26", "CDC27", "CFT1", "CFT2", "DCP1", "DOC1", "FIP1", "GCN5", "GLC7", "HFI1", "KEM1", "LSM1", "LSM2", "LSM3", "LSM4", "LSM5", "LSM6", "LSM7", "LSM8", "MPE1", "NGG1", "PAP1", "PAT1", "PFS2", "PTA1", "PTI1", "REF2", "RNA14", "RPN1", "RPN10", "RPN11", "RPN13", "RPN2", "RPN3", "RPN5", "RPN6", "RPN8", "RPT1", "RPT3", "RPT6", "SGF11", "SGF29", "SGF73", "SPT20", "SPT3", "SPT7", "SPT8", "TRA1", "YSH1", "YTH1") # Optional expression (1=UP, -1=DW): genesYeastExpr <- setNames(c(rep(1,29), rep(-1,30)), genesYeast) # Submit query jobID <- fea_gtLinker(geneList=genesYeast,organism="Sc") jobID ### Get results from FEA: jobID <- 3907019 # job ID of the query results <- fea_gtLinker_getResults(jobID=jobID) # To continue the workflow... (see help for further details)) incidMat <- fea2incidMat(results) functionalNetwork(incidMat) # Or full report FGNet_report(results, geneExpr=genesYeastExpr) ## End(Not run)