Description Usage Arguments Value Examples
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.
1 2 |
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. |
an object of the same type as 'ranged', but only containing the rows that were within the specified bounds
1 2 3 4 5 6 7 8 | 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]
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.