pf_analysis: Protected fragment analysis
In Bankso/SCAR: SpLiT-ChEC analysis with R

pf_analysis

R Documentation

Protected fragment analysis

Protected fragment analysis

pf_analysis(
  SCAR_obj,
  outdir = getwd(),
  in_bam = NA,
  in_bg = NA,
  thresh = 0,
  bed_file = bed_file
)

`SCAR_obj`	SCAR object.
`outdir`	Output directory.
`in_bam`	path to an input bam, leave blank if none
`in_bg`	path to an input bedgraph, leave blank if none
`thresh`	a cutoff for 'low' signal. Coverage regions under this threshold will be compared to the input bam file as 'low signal' regions
`bed_file`	A bed file of regions to be checked for local low signal sites in aligned bams