Boxplot of normalized PSI stratified by genotypes for sQTL.

xQTLvisual_sqtlExp(
  variantName = "",
  phenotypeId = "",
  variantType = "auto",
  tissueSiteDetail = "",
  axis_text_size = 1.3,
  axis_title_size = 1.3,
  title_size = 1.4,
  xlab_text = "Genotypes",
  ylab_text = "Norm.Intron-Excision Ratio",
  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".
phenotypeId: A character string. Format like: "chr1:497299:498399:clu_54863:ENSG00000239906.1"
variantType: (character) options: "auto", "snpId" or "variantId". 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: (character) Lable for x-axis
ylab_text: (character) Lable for x-axis
ylim_v: (numeric vector) Set scale limits
title_text: (character) Title of the plot
jitter_color: (A character vector) Set the point color.

Value

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

Examples

expSqtl <-xQTLvisual_sqtlExp(variantName="chr11_66561248_T_C_b38",
          phenotypeId ="chr11:66348070:66353455:clu_8500:ENSG00000255468.6",
          tissueSiteDetail="Skin - Sun Exposed (Lower leg)")