Guitar (version 1.10.0)

getNeighborhood: getNeighborhood

Description

This functon extract the neighborhood DNA regions of a GRangesList object. The neighborhood DNA regions represent the promoter region (5'end) and complementary DNA region on the 3'end, which we call "Tail" here. The 5'end neighborhood DNA can often be useful as a kind of negative control region that is not associated with a clear biological function.

This function is different from the "promoters" function available from GenomicRanges R package, which is designed to extract only the promoter region (5' side DNA), but not the 3' side DNA region.

Usage

getNeighborhood(comp, side = 5, Width = 1000)

Arguments

comp

a GRangesList object, whose 5' or 3' side DNA neighborhood will be extracted.

side

either 5 or 3. When it is 5, the promoter region of the GRangesList object will be extracted; if it is 3, the region on the 3' side complementary to the promoter region will be extracted.

Width

The width of the neighborhood region will be extracted. default: 1000

Value

A GRangesList, of the same length as the input, will be returned. You may use unlist to convert it into a GRanges object.

Details

All inner list elements of the input GRangesList object must have the same strand

Examples

gr1 <-
  GRanges(seqnames = "chr2", ranges = IRanges(3000, 6000),
          strand = "+", score = 5L, GC = 0.45)
gr2 <-
  GRanges(seqnames = c("chr1", "chr1"),
          ranges = IRanges(c(7000,13000), width = 3),
          strand = c("+"), score = 3:4, GC = c(0.3, 0.5))
grl <- GRangesList("gr1" = gr1, "gr2" = gr2)
promoter <- getNeighborhood(grl,5)
promoter
promoter_GRanges <- unlist(promoter)
promoter_GRanges