This function takes paired-end fragments, extract the "cuts" (i.e. extremities) and plot the footprint profile over a set of GRanges.

plotFootprint(
  frags,
  targets,
  split_strand = FALSE,
  plot_central = TRUE,
  xlim = c(-75, 75),
  bin = 1,
  verbose = 1
)

Arguments

frags

GRanges, the paired-end fragments

targets

GRanges, the loci to map the fragments onto

split_strand

Boolean, should the + and - strand be splitted?

plot_central

plot grey rectangle over the loci

xlim

numeric vector of length 2, the x limits of the computed Vmat

bin

Integer, bin used to smooth the gootprint profile

verbose

Integer

Value

A footprint ggplot

Examples

data(bam_test) data(ce11_proms) plotFootprint(bam_test, ce11_proms)
#> - Getting cuts
#> - Getting cut coverage
#> - Getting cut coverage / target
#> - Reformatting data into matrix
#> - Plotting footprint