extract_summary: Perform PCA analysis
In scfurl/seqGlue: Makes sequencing data come together like glue

extract_summary

R Documentation

Perform PCA analysis

Description

Perform PCA analysis

Usage

extract_summary(
  bigWigs = NULL,
  bed = NULL,
  binSize = 50,
  top = 1000,
  nthreads = 4,
  ucsc_assembly = NULL,
  ucsc_startFrom = "start",
  ucsc_up = 2500,
  ucsc_down = 2500,
  custom_names = NULL
)

Arguments

`bigWigs`	bigWig files. Default NULL. Required.
`bed`	bed file or a data.frame with first 3 column containing chromosome, star, end positions.
`binSize`	bin size to extract signal. Default 50 (bps). Should be >1
`nthreads`	Default 4
`ucsc_assembly`	If ‘bed' file not provided, setting 'ucsc_assembly' to ref genome build will fetch transcripts from UCSC genome browser. e.g; ’hg19'
`ucsc_startFrom`	Default "center". Can be "center", "start" or "end"
`ucsc_up`	extend upstream by this many bps from 'startFrom'. Default 2500
`ucsc_down`	extend downstream by this many bps from 'startFrom'. Default 2500
`custom_names`	Default NULL and Parses from the file names.