annotateHits: Annotates Hits by Genomic Features

In pryabinin/ComplexID: Integrated Hit Annotations and Random Walk of Complex Network

Description

Annotates Hits by Genomic Features

Usage

annotateHits(Hits, promoterRange = 1e+05, upstream = 0, downstream = 0,
  geneBody = T, promoters = T, promoterTissues = "all", utr = T,
  eqtl = T, eqtlTissues = "all", enhancers = T, enhancerTissues = "all",
  non_proteins = F, loopDist = 0, useAllTSS = T)

Arguments

Hits	Granges object with two meta data columns, or a matrix or data frame with at least 5 columns. If it is a Granges object, then the first meta data column is the site's name. The second meta data columns is a phenotype that the site is associated with. If it is a matrix or data frame, then the first column must be the Hit's name, the second column must be chromosome designation, the third column must the starting base pair position, the fourth column must be the ending base pair position (equal to starting bp position for a standard SNP) and the fifth column must a phenotype that the site is associated with. For both Grange objects and matrices/dataframes, each entry/row corresponds to one site that is associated to one phenotype. If a site is associated in multiple phenotypes then there would be multiple entries for the same site but all with different values in the phenotype column
promoterRange	single integer greater than or equal to zero. How many bases to look upstream of a TSS of a gene in order to find a promoter region for a gene.
upstream	single integer. By default 0. How far upstream of a transcription start site a hit can be for it to be annotated to that gene. A NULL value is equivalent to a value of zero (no upstream sites will be annotated to a gene unless they lie in a promoter region, see promoterRange parameter).
downstream	single integer. By default 0. How far downstream of a transcription start site a hit can be for it to be annotated to that gene. A NULL value is equivalent to a value of zero (no downstream sites will be annotated to a gene).
geneBody	TRUE or FALSE, by default TRUE. If TRUE, then hits will be annotated to the bodies (exons and introns) of protein coding genes. If FALSE, hits will not be annotated to those regions.
promoters	TRUE or FALSE, by default TRUE. If TRUE, then hits will be annotated to promoter regions. If FALSE, hits will not be annotated to promoter regions.
promoterTissues	character vector, by default is "all". If "all", then all promoters from all tissues will be included in the annotation, otherwise, only promoter regions from tissues specified by promoterTissues will be used for annotation.
utr	TRUE or FALSE. If TRUE then it will look for hits in the 3' and 5' UTRs of genes, otherwise it will not.
eqtl	TRUE or FALSE. By default TRUE. If TRUE, then hits may be mapped to eQTL loci, and therefore genes effected by those eQTLs be designated as associated to those hits.
eqtlTissues	character vector, by default is "all". If "all", then all eQTLs from all tissues will be included in the annotation, otherwise, only eQTL sites from tissues specified by promoterTissues will be used for annotation.
enhancers	TRUE or FALSE. By default TRUE. If TRUE, then hits may be mapped to enhancer loci and linked to genes via looping structures and promoters
enhancerTissues	character vector, by default is "all". If "all", then all enhancers from all tissues will be included in the annotation, otherwise, only enhancers regions from tissues specified by promoterTissues will be used for annotation.
non_proteins	TRUE or FALSE. By default FALSE. If TRUE then hits may be mapped to non-protein regions, if FALSE then that annotation will not be used.
loopDist	single integer. By default 0. The maximum allowable distance that an enhancer or promoter can be from a looping region to be annotated to it.
useAllTSS	TRUE or FALSE. By default TRUE. If TRUE, then all unique transcription start sites will be considered when looking at upstream regions of a gene (for promoters and upstream regions). If FALSE, it will a single start site for a gene, namely the start of the gene.

pryabinin/ComplexID documentation built on May 8, 2019, 1:14 p.m.