coverageGeneBodyScaled: coverageGeneBodyScaled

In tschauer/HelpersforChIPSeq:

Description

creates a matrix from a coverage vector RleList. The matrix is aligned to start and end genomic coordinates and values in between (e.g. gene body) are scaled (re-sized) to a fixed length.

Usage

coverageGeneBodyScaled(
  my_coverage,
  my_coordinates,
  margin_outer = 500,
  margin_inner = 500,
  genebody_scaler = 1000
)

Arguments

my_coverage	coverage vector (RleList)
my_coordinates	data.frame of genomic coordinates with columns named as "chr", "start", "end","strand".
margin_outer	integer of outer window in bp, default 500.
margin_inner	integer of inner window in bp, default 500.
genebody_scaler	integer of gene body length to be scaled to, default 1000.

Value

output matrix with each row corresponding a gene and each column a genomic position.

See Also

coverageWindowsCenteredStranded

Examples

my_coverage <- RleList("chrI"=  rpois(100000, 10),
                      "chrII"= rpois(150000, 10))
my_coverage

my_coordinates <- data.frame(chr = c("chrI", "chrII", "chrIII"),
                            start = c(1000, 4000, 200),
                            end = c(5000, 14000, 2000),
                            strand = c("+", "-", "-"),
                            row.names = c("gene1", "gene2", "gene3"))
my_coordinates

my_mat <- coverageGeneBodyScaled(my_coverage = my_coverage,
                                my_coordinates = my_coordinates)
my_mat[,1:5]

tschauer/HelpersforChIPSeq documentation built on Nov. 15, 2021, 9:55 a.m.