findNeighbors: A function to locate neighboring genes within a defined range...

In annotate: Annotation for microarrays

Description

Give a data package with mappings between Entrez Gene IDs and their locations on chromosomes, this function locates genes that are within a defined range on a given chromosome. If a Entrez Gene ID is passed as one of the arguments, genes located will be neighbors to the gene represented by the Entrez Gene ID within a defined range on the chromosome the target gene resides

Usage

findNeighbors(chrLoc, llID, chromosome, upBase, downBase, mergeOrNot = TRUE)
checkArgs(llID, chromosome, upBase, downBase)
findChr4LL(llID, chrEnv, organism)
getValidChr(organism)
getBoundary(loc, base, lower = TRUE)
weightByConfi(foundLLs)

Arguments

chrLoc	chrLoc a character string for the name of the data package that contains mappings between Entrez Gene IDs and their locations on chromosomes. For each chromosome, there assumed to be mappings for the start and end locations of genes represented by Entrez Gene IDs. The data package needs to be built using chrLocPkgBuilder of AnnBuilder
llID	llID a character string for the Entrez Gene ID representing a gene whose neighbors are sought. llID can be missing
chromosome	chromosome a character string for the number of the chromosome of interest. chromosome is only required for locating genes within a range on the chromosome
upBase	upBase a numeric or character string for the number of base pairs that defines the upper limit of the range to locate genes. If neighbors of a given gene is sought, the value will be the distance in number of base pairs from the target gene upstream, to which search for genes will be conducted. Otherwise, the value will be the upper limit in number of base pairs from the p arm, to which search for genes will be conducted
downBase	downBase a numeric or character string for the number of base pairs that defines the lower limit of the range to locate gene. If neighbors of a given gene is sought, the value will be the distance in number of base pairs from the target gene downstream, to which search for genes will be conducted. Otherwise, the value will be the lower limit in number of base pairs from the p arm, to which search for genes will be conducted
organism	organism a character string for the name of the organism of interest
chrEnv	chrEnv an environment object with keys for Entrez Gene IDs and values for the chromosomes where genes reside
loc	loc a numeric of character string for the chromosomal location of gene of interest
base	base either a downBase or upBase
lower	lower a boolean indicating whether the lower or upper boundary of search limit is sought
mergeOrNot	mergeOrNot a boolean to indicate whether gene found up and down streams will be merged (TRUE)
foundLLs	foundLLs a vector of character strings for Entrez Gene IDs

Details

A chrLoc data package can be created using function chrLocPkgBuilder of AnnBuilder, in which Entrez Gene IDs are mapped to location data on individual chromosomes.

Genes are considered to be neighbors to a given target gene or within a given range when the transcription of genes start and end within the given range.

findNeighbors, checkArgs, findChr4LL, getValidChr, and getBoundary are accessory functions called by findNeighbors and may not have real values outside.

Value

The function returns a list of named vectors. The length of the list is one when genes in a given region are sought but varies depending on whether a given gene can be mapped to one or more chromosomes when neighboring genes of a target gene are sought. Names of vector can be "Confident" when a gene can be confidently placed on a chromosome or "Unconfident" when a gene can be placed on a chromosome but its exact location can not be determined with great confidence.

Author(s)

Jianhua Zhang

References

http://www.genome.ucsc.edu/goldenPath/

Examples

if(require("humanCHRLOC")){
   findNeighbors("humanCHRLOC", "51806", 10, upBase = 600000, downBase = 600000)
}else{
   print("Can not find neighbors without the required data package")
}

Example output

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: XML
Loading required package: humanCHRLOC
[1] "Can not find neighbors without the required data package"
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'humanCHRLOC'

annotate documentation built on Nov. 8, 2020, 8:14 p.m.