checkSex: Function checkSex

In jrthompson54/DGE.Tools2: A function library to facilitate Differential Gene Expression Analysis

Description

Take a DGEobj as input and plot expression of XIST vs the highest expressed Y chr gene.

Usage

checkSex(
  dgeObj,
  species,
  sexCol,
  labelCol,
  showLabels = FALSE,
  chrX = "X",
  chrY = "Y",
  baseFontSize = 14,
  orig = TRUE,
  debug = FALSE
)

Arguments

dgeObj	A DGEobj (Required)
species	One of "human", "mouse", "rat"
sexCol	Character string name of the sex annotation column in the design table within the dgeObj (optional)
labelCol	Character string name of the design column to use to label points with ggrepel (optional if showLabels=FALSE)
showLabels	Set TRUE to turn on ggrepel labels (default = FALSE)
chrX	Character string name of the X chromosome in the gene annotation within the geneData object (Default = "X")
chrY	Character string name of the Y chromosome in the gene annotation within the geneData object (Default = "Y")
baseFontSize	Sets the base font size for ggplot themes (Default = 14)
orig	Set to FALSE to use your filtered DGEobj data. Set to TRUE to use original unfiltered data (Default = TRUE)
debug	Default=FALSE. Set to TRUE to open a debug browser when entering this function

Details

This uses the original unfiltered data by default. This is because Y-linked genes are often below the low intensity threshold in tissues other than testes. Nevertheless, there are usually enough reads for the plot to be interpretable.

Value

A ggplot object

Author(s)

John Thompson, [e-mail]

Examples

   checkSex(dgeObj, species="human")

jrthompson54/DGE.Tools2 documentation built on May 12, 2021, 8:47 p.m.