DAEQTL plot

A simple wrapper around a ggplot2 plot showing allelic expression ratios for two groups of samples: homozygous and heterozygous. This is a handy function to quickly inspect the data underlying each DAEQTL mapping test.

Usage

daeqtl_plot(
  ae_hom,
  ae_het,
  dae_threshold = log2(1.5),
  min_n_hom = 2L,
  min_n_het = 2L,
  dae_threshold_linetype = "dashed",
  xlab = "Candidate SNP zygosity",
  ylab = "DAE SNP allelic expression (log-ratio)",
  ylim = NULL
)

Arguments

ae_hom

Numeric vector of AE ratios of the DAE SNP. Each element of the vector refers to a sample that is homozygous (hom) for the candidate SNP.

ae_het

Numeric vector of AE ratios of the DAE SNP. Each element of the vector refers to a sample that is heterozygous (het) for the candidate SNP.

dae_threshold

An allelic expression (AE) threshold (in log-scale). A sample showing an absolute AE greater than dae_threshold is considered "technically" differential allelic expressed, meaning that the imbalance observed is not below the limit of detection. Adjustment made to this parameter should depend on the experimental assay sensitivity.

min_n_hom

Minimum number of samples in the homozygous group to be considered eligible for statistical testing.

min_n_het

Minimum number of samples in the heterozygous group to be considered eligible for statistical testing.

dae_threshold_linetype

Line type for the DAE threshold. See Line type for options.

xlab

Title of the x-axis.

ylab

Title of the y-axis.

ylim

A two element vector specifying the y-axis limits.

Examples

ae_hom <- c(1.9, 2.1, 2 , 1.5, 1.4)
ae_het <- c(0.3, 0.6, 0.7)
daeqtl_plot(ae_hom = ae_hom, ae_het = ae_het)