query-methods: Query enrichment in geneset through multiple eQTL sets.

In StanleyXu/loci2path: Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs

Description

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.

Usage

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)

Arguments

query.gr	a GenomicRange object, representing query regions
loci	a list of eqtlSet; each member should be an eqtlSet; Or it can be a single eqtlSet.
path	Pathways or geneSets to be tested for enrichment
...	additional params
N	the total number of non-N nucleotides in the genome; default N=2897310462 is for hg19
verbose	bool; whether to show eqtlSet/geneSet summary information; default is FALSE
permutation	bool; whether to calculate rank-based permutation; default is FALSE
parallel	bool; whether to enable parallel computing; default is FALSE

Details

The user need to specify

1. Query region;

2. 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.

3. 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 path is 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 (getMat, getHeatmap, 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 of eqtlSet.

If user input one eQTL set as argument loci, a simple list object will be returned for specific research purpose.

Value

a data.frame showing the tissue enrichment of the query regions by binomial test.

a list; result.table is the major result table showing enrichment assessment; cover.gene is the vector showing the genes from the eqtl Sets covered by the query region(s)

a loci2pathResult class object

See Also

loci2pathResult

Examples

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)

StanleyXu/loci2path documentation built on Sept. 11, 2019, 8:21 a.m.