ifs_score: Calculate raw IFS scores

ifs_scoreR 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.


epifluidlab/cragr documentation built on Jan. 29, 2024, 5:35 p.m.