This is the main function for loci2path query. Query can be made on either pathway enrichment or tissue-specificity, depending on the input Class. See Details for more.
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query(query.gr, loci, path, ...) ## S4 method for signature 'GenomicRanges,list,ANY' query(query.gr, loci, N = 2897310462) ## S4 method for signature 'GenomicRanges,eqtlSet,geneSet' query(query.gr, loci, path, verbose = FALSE, permutation = FALSE) ## S4 method for signature 'GenomicRanges,list,geneSet' query(query.gr, loci, path, parallel = FALSE, verbose = FALSE, permutation = FALSE)
a GenomicRange object, representing query regions
a list of eqtlSet; each member should be an eqtlSet; Or it can be a single eqtlSet.
Pathways or geneSets to be tested for enrichment
the total number of non-N nucleotides in the genome; default N=2897310462 is for hg19
bool; whether to show eqtlSet/geneSet summary information; default is FALSE
bool; whether to calculate rank-based permutation; default is FALSE
bool; whether to enable parallel computing; default is FALSE
The user need to specify
loci; one or more eQTL set; this is usually more than one eQTL set. Only multiple eQTL set derived from different cells/tissues will show cell/tissue specificity.
path; pre-defined Pathways, or gene sets. the gene sets that enrichment tests would be performed to.
loci must be provided;
path is optional. When
missing, the tissue-specificity query for the regions is performed.
The most common case for
loci is an eQTL set list.
This function perform enrichment test between one eQTL set and a group of
gene sets. Usually query are based on eQTL set list, rather than only one
eQTL set. Several result exploring functions (
getPval, etc...) are designed for query result
from eQTL set list and gene sets. The class
loci2pathResult is also
designed for eQTL set list query result only. The result returns a
loci2pathResult only the class of
loci is a list
If user input one eQTL set as argument
loci, a simple
list object will be returned for specific research purpose.
a data.frame showing the tissue enrichment of the query regions by binomial test.
result.table is the major result table showing
cover.gene is the vector showing the genes from the eqtl Sets
covered by the query region(s)
loci2pathResult class object
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gr.tissue <- query(query.gr, eset.list) #build one eqtlset skin.eset <- eset.list$Skin #query one egset res.one <- query(query.gr, skin.eset, biocarta) #enrichment result table res.one$result.table #all the genes associated with eQTLs covered by the query region res.one$cover.gene result <- query(query.gr=query.gr, loci=eset.list, path=biocarta) #enrichment result table resultTable(result) #all the genes associated with eQTLs covered by the query region coveredGene(result)
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