xQTLvisual_eqtlExp: Boxplot of normalized expression stratified by genotypes for...

In xQTLbiolinks: An R Package for Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'

Boxplot of normalized expression stratified by genotypes for eQTL.

Description

Boxplot of normalized expression stratified by genotypes for eQTL.

Usage

xQTLvisual_eqtlExp(
  variantName = "",
  gene = "",
  variantType = "auto",
  geneType = "auto",
  tissueSiteDetail = "",
  axis_text_size = 1.3,
  axis_title_size = 1.3,
  title_size = 1.4,
  xlab_text = "Genotypes",
  ylab_text = "Normalized expression",
  ylim_v = NULL,
  title_text = "",
  jitter_color = NULL
)

Arguments

variantName	(character) name of variant, dbsnp ID and variant id is supported, eg. "rs138420351" and "chr17_7796745_C_T_b38".
gene	(character) gene symbol or gencode id (versioned or unversioned are both supported).
variantType	(character) options: "auto", "snpId" or "variantId". Default: "auto".
geneType	(character) options: "auto","geneSymbol" or "gencodeId". Default: "auto".
tissueSiteDetail	(character) details of tissues in GTEx can be listed using tissueSiteDetailGTExv8 or tissueSiteDetailGTExv7
axis_text_size	(numberic) text size of the axis labels
axis_title_size	(numberic) text size of the axis title
title_size	(numberic) text size of the title of the plot
xlab_text	Lable for x-axis
ylab_text	for y-axis
ylim_v	Set scale limits
title_text	Title of the plot
jitter_color	(A character vector) Set the point color.

Value

A list containing eQTL detail, expression profile and a ggplot object.

Examples

expEqtl<-xQTLvisual_eqtlExp(variantName="rs3778754", gene ="IRF5",
                            tissueSiteDetail="Whole Blood", xlab_text="Genotypes",
                            ylab_text="Expression", ylim_v=c(-2,2),
                            axis_text_size=1.3, axis_title_size=1.3, title_size=1.4,
                            title_text="Genotype-expression",
                            jitter_color=c("#83bea5", "#e09069","#8f9dc6") )

xQTLbiolinks documentation built on Sept. 15, 2023, 1:06 a.m.