DEXSeqAnalysis: DEXSeqAnalysis

In adamstruck/RECD: Repeat Exansion & Contraction Detection

Description

Try to detect repeats that have gotten longer than the typical inner mate distance

Usage

  DEXSeqAnalysis(counts_table, fdata_table, pheno_table,
    condition, grouping, output_file)

Arguments

countsTable
fdata
pheno_table
condition	condition to base the differential analysis on.
grouping	list specifying a specific variable name and level to subset the data by. Only samples that have this trait (level) will be examined. [ Example: grouping = list(name="Tissue.Group.Oncology", level="Colon") ]
output_file	path to and name of file to output results to.

Details

Uses the DEXSeq package to try and detect differential read class frequencies (facing versus flanking) between tumor and normal samples.

Value

TSV file

Author(s)

Adam Struck - Intern

adamstruck/RECD documentation built on May 10, 2019, 5:51 a.m.