humarray (version 1.2)

nearest.gene: Retrieve the 'n' closest GENE labels or positions near specified locus

Description

Retrieve the 'n' closest GENE labels or positions near specified locus

Usage

nearest.gene(chr, pos, n = 1, side = c("either", "left", "right"),
  ids = TRUE, limit = NULL, build = NULL, ga = NULL)

Arguments

chr

integer, chromosome, should be a number from 1 to 25, where 23,24,25 are X,Y,MT

pos

integer, genomic position, should be between 1 and the length of the chromosome 'chr'

n

integer, the number of nearest GENEs to seek, if there aren't enough in the annotation then NAs will fill the gaps to force the return value length to equal 'n'

side

character, can be 'either', 'left' or 'right' and specifies which side of the 'pos' to look for nearest genes (where left is decreasing genomic position and right is increasing)

ids

logical, if TRUE will return GENE labels, or if FALSE will return the chromosome positions of the genes

limit

integer, a limit on the maximum distance from the position 'pos' can be specified

build

integer whether to use build 36/37 parameters, 36/37 is preferred, but can enter using any form recognised by ucsc.sanitizer()

ga

RangedData object, e.g, result of get.gene.annot(); gene annotation to save download time if repeatedly calling this function

Value

Set of GENE ids (when ids=TRUE), or otherwise genomic positions within chromosome 'chr'. If the number of gemes on the chromosome or the bounds of the 'side' and 'limit' parameters restrict the number returned to less than 'n' then the return value will be padded with NAs.

See Also

expand.nsnp, nearest.snp, get.gene.annot

Examples

# NOT RUN {
nearest.gene(1,159000000,n=10) # return ids
nearest.gene(1,159000000,n=10,build=37)
nearest.gene(1,159000000,n=10,build=36,ids=FALSE) # return positions
nearest.gene(1,159000000,n=10,build=37,ids=FALSE)
nearest.gene(6,25000000,n=10,build=37,ids=FALSE,side="left")  # only genes to the left of the locus
nearest.gene(6,25000000,n=10,build=37,ids=FALSE,side="right") # only genes to the right of the locus
# }