auto.rats: Autosomal Ratios (auto.rats)

In genejockey33000/typGumbo: Scripts and Pipelines for RNAseq Analysis

Autosomal Ratios (auto.rats)

Description

For each sample, calculates ratio of normalized expression for all measurements from each autosome to all other autosomes (i.e. autosome ratio). Then compares ratios across all samples for each chromosome. Can detect severe chromosomal abnormalities (i.e. chromosomal duplication or loss). Outputs data frame of all ratios with column for each chromosome and a pdf containing all ratio plots for chr1:chr22. Pdfs are written to a sub-folder named 'plots'

Usage

auto.rats(typ.obj, color.by = NULL)

Arguments

typ.obj	typ objects of type 'typ.gene' or 'typ.trans'
color.by	OPTIONAL Specify column in object meta data to color bar plots (i.e. "sex" or "karyotype")

Value

matrix of ratios, pdf containing plots

genejockey33000/typGumbo documentation built on July 20, 2023, 11:45 p.m.