getAnnotations: getAnnotations

In chrisamiller/readDepth: Find regions of genomic copy number loss and gain from short reads

Description

connect to the annotation repository and retrieve the appropriate annotation files

Usage

  getAnnotations(readLength, sex, genome="hg18", bs=FALSE)

Arguments

readLength	the average length of the reads, in bp.
sex	either "male" or "female"
genome	genome build, in the form of "hg18"
bs	whether the reads are the result of bisulfite sequencing (TRUE/FALSE)

Details

As of v1.0, the repo contains info for both hg18 and hg19 with read lengths of: 27, 36, 55, 76, 100, and 200.

Bisulfite annotations have only been calculated 76bp reads on hg18

Instructions for creating your own annotation files for parameter sets not listed here are available at: https://xfer.genome.wustl.edu/gxfer1/project/cancer-genomics/readDepth/index.html

Examples

  #  library(readDepth)
  #  getAnnotations(readLenght=76, sex="male", genome="hg19")

chrisamiller/readDepth documentation built on June 16, 2021, 2:05 p.m.