findNeighbors {annotate} | R Documentation

## A function to locate neighboring genes within a defined range around a target gene represented by a LocusLink id

### Description

Give a data package with mappings between LocsuLink ids and their locations on chromosomes, this function locates genes that are within a defined range on a given chromosome. If a LocusLink id is passed as one of the arguments, genes located will be neighbors to the gene represented by the LocusLink 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 LocusLink ids and their locations on chromosomes. For each chromosome, there assumed to be mappings for the start and end locations of genes represented by LocusLink ids. The data package needs to be built using chrLocPkgBuilder of AnnBuilder
`llID` | `llID` a character string for the LocusLink id representing a gene whose nighbors 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 sourght, 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 locat gene. If neighbors of a given gene is sourght, 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 LocusLink 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 LocusLink ids

### Details

A chrLoc data package can be created using function chrLocPkgBuilder of AnnBuilder, in which locusLink 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 rwgion are sought but varies depending on whether a given gene can be mapped to one or more chromosomes when neighoring 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.

### Note

This function is part of the Bioconductor project at Dana-Farber Cancer Institute to provide bioinformatics functionalities through R

### Author(s)

Jianhua Zhang

### References

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

### Examples

    if(require("humanCHRLOC")){
       findNeighbors("humanCHRLOC", "10228", upBase = 600000, downBase = 600000)
    }else{
       print("Can not find neighbors without the required data package")
    }

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