ifs_score: Calculate raw IFS scores
In haizi-zh/cragr: R package for CRAG

ifs_score

R Documentation

Calculate raw IFS scores

Description

Calculate raw IFS scores from coverage and fragment length, and do the mappability filtering.

Usage

ifs_score(
  fragment_data,
  interval = NULL,
  chrom = NULL,
  window_size = 200L,
  step_size = 20L,
  gc_correct = TRUE,
  blacklist_region = NULL,
  high_mappability_region = NULL,
  min_mapq = 30L,
  min_fraglen = 50L,
  max_fraglen = 1000L,
  exclude_soft_clipping = FALSE
)

Arguments

`fragment_data`	A `GRanges` data frame containing cfDNA fragment data.
`interval`	Intervals against which IFS scores should be calculated
`chrom`	Calculate IFS scores for certain chromosomes. If `NULL`, all chromosomes in `fragment_data` will be used.
`window_size`	Width of the sliding window. Must be multiples of `step_size`.
`step_size`	Incremental steps of the sliding window.
`gc_correct`	Logical value. Whether to perform GC correction. If `TRUE`, the corresponding `BSgenome` should be present. Currently, only support `BSgenome.Hsapiens.1000genomes.hs37d5`.
`blacklist_region`	Those fragments whose midpoint fall within any of the excluded regions will not be used in the analysis. `blacklist_region` can be either a character vector that contains the names of the files defining the regions (should be in BED format), a `GRanges` object, or a list of `GRanges` objects.
`high_mappability_region`	Regions with high mappability scores. Only the windows within such regions with be used in the analysis. Must be a `GRanges`, or path of the BED file path.
`min_mapq`	Exclude fragments whose `MAPQ` scores are smaller than `min_mapq`.
`min_fraglen`	Exclude fragments shorter than `min_fraglen`.
`max_fraglen`	Exclude fragments longer than `max_fraglen`.
`exclude_soft_clipping`	For fragments with leading soft clipping, their inferred lengths are less reliable. If `TRUE`, such fragments will be excluded from the analysis. `cigar1` and `cigar2` should be present in the dataset.