humarray (version 1.2)

in.window: Select all ranges lying within a chromosome window

Description

Input a ranged object (ie., GRanges or RangedData) and this function will return the subset from chromosome 'chr' and within the base-pair range specified by 'pos', in units of 'unit'. By default ranges with ANY overlap are returned, but it can be specified that it must be full overlap. Duplicates can be removed.

Usage

in.window(ranged, chr, pos, full.overlap = F, unit = c("b", "kb", "mb",
  "gb"), rmv.dup = FALSE)

Arguments

ranged

GRanges or RangedData object

chr

a chromosome, e.g, 1,2,3,...,22,X,Y,XY,MT or however chromosomes are annotated in 'ranged'

pos

a numeric range (length 2), with a start (minima) and end (maxima), specifying the window on the chromosome to select ranges from, base-pair units are specified by 'unit'.

full.overlap

logical, the default is to return objects with ANY overlap with the window, whereas setting this as TRUE, will only return those that fully overlap

unit

the unit of base-pairs that 'pos' is using, eg, "b", "kb", "mb", "gb"

rmv.dup

logical, whether to remove duplicate ranges from the return result. The default is not to remove duplicates.

Value

an object of the same type as 'ranged', but only containing the rows that were within the specified bounds

Examples

# NOT RUN {
require(GenomicRanges)
iG <- get.immunog.locs()[2,] # select the 2nd iG region
ciG <- chrm(iG)  #  get the chromosome
posiG <- c(start(iG),end(iG)) # get the region start and end
rr <- rranges(10000) # create a large random GRanges object
in.window(rr,chr=ciG,pos=posiG) # set with ANY overlap of iG
in.window(rr,chr=ciG,pos=posiG,TRUE) # set with FULL overlap of iG
in.window(rr,chr=6,pos=c(25,35),unit="mb") # look between 25 - 35 MB on chr6 [ie, MHC]
# }