make_tracks_opts: Generate coverage tracks
In Bankso/SCAR: SpLiT-ChEC analysis with R

make_tracks_opts

R Documentation

Generate coverage tracks

Description

Generate coverage tracks

Usage

make_tracks_opts(
  SCAR_obj,
  outdir = getwd(),
  compare = FALSE,
  scale_method = NA,
  MNase = FALSE,
  comp_op = "log2",
  bin_size = 1,
  normalize_using = NA,
  genome_size = NA,
  skip_non_covered = NA,
  min_fragment = NA,
  max_fragment = NA,
  extend_reads = NA,
  scale_factors = NA,
  split_strands = NA,
  library_type = NA,
  center_reads = NA,
  out_type = NA,
  temp_dir = "./temp"
)

Arguments

`SCAR_obj`	SCAR object.
`outdir`	Output directory.
`compare`	TRUE or FALSE - should bamCompare or bamCoverage be performed
`scale_method`	Default is 'readCount', other options are 'SES' and 'NONE'
`MNase`	Calculate nucleosome positions for the input BAMs? Paired only
`comp_op`	Operation for bamCompare
`bin_size`	Bin size for coverage summary.
`normalize_using`	Either 'CPM' or 'RPGC'/'RPKM'.
`genome_size`	Effective genome size, req'd for RPGC/RPKM.
`skip_non_covered`	Should regions without coverage be skipped.
`min_fragment`	Minimum fragment length.
`max_fragment`	Maximum fragment length.
`extend_reads`	Distance to extend single-end reads. Set to NA to not extend reads.
`scale_factors`	Takes a named vector, with the name being the sample name, and the value being the scale factor. If set will override 'normalize_using' option.
`split_strands`	For RNA-seq, whether to split the strands into positive and minus strand files.
`library_type`	If split_strands is TRUE, specify library chemistry as either 'dUTP' or 'ligation'.
`center_reads`	Should reads be centered based on fragment length? Helps with signal around enriched regions
`out_type`	Output file format, bedgraph or bigwig
`temp_dir`	Temporary directory to write files to.