Tn5 sequence preference of one sample — computeKmerBias • chromTFR

The enrichment of every k-mer at the observed cut sites over its frequency in the accessible genome. The k-mer is centred on the cut and the weights are symmetrised over the two strands, because both fragment ends are counted as insertions.

Usage

computeKmerBias(
  ins,
  regions,
  genome,
  k = 6L,
  max.ins = 2e+06,
  chunk = 1e+05,
  bg = NULL
)

Arguments

ins: A GRanges of insertion sites with a score column.
regions: A GRanges of the accessible regions.
genome: A BSgenome object.
k: Length of the k-mer.
max.ins: Number of insertion sites drawn for the estimate.
chunk: Number of sites read from the genome at a time.
bg: Background counts from kmerBackground, or NULL to count them here.

Value

A named numeric vector of k-mer weights.

Examples

if (FALSE) { # \dontrun{
bias <- computeKmerBias(ins, peaks, Hsapiens, bg = bg)
} # }