Package index • QTLretrievR

Primary functions for peak calling, haplotype effect analysis, and mediation

genoprobably(): Convert GBRS tsv genome probabilities to genoprobs format.
mugaprobs(): Convert and process MUGA probabilities to qtl2 format
runQTL(): Wrapper function to generate mapping, peaks, mediation, and effects data
mapQTL(): Generate mapping data and peaks for QTL analysis
gxeQTL(): Generate mapping data and peaks for G x E QTL analysis
LOD_thld(): Determine significant and suggestive LOD thresholds
qtl_effects(): Calculate founder effects for significant peaks
modiFinder(): Prepare and run mediation for a set of QTL peaks
multi_modiFinder(): Prepare and run between phenotype mediation for a set of QTL peaks with provided expression data.

Functions used for plotting and visualizations

plot_eqtlmap(): Plot QTL maps (peak vs gene)
transbands(): Identify distal hotspots above a suggestive and significant LOD score.
hsHapEffects(): Map founder haplotype effects for a given hotspot.
medPlot_hotSpot(): Identify top mediators within a hotspot (molecular QTL)
medPlot_single(): Identify mediators for provided features +/- x Mb from a given position on a given chromosome
hsPeakPlot(): Plot an individual peak or Principal Component of a hotspot.
tailWag(): Create a plot with founder effects for a given phenotype
peak_plot(): Plot peaks associated with specific genes.

Datasets built into QTLretrievR for examples or use in mapping

Functions run during mapQTL that may be useful after the factt

annotatePeaks(): Interpolate peak positions and attach annotations
interp_bp(): interp_bp
interp_cM(): interp_cM
check_data(): Checking the inputted data for QTLretrievR
split_map(): Background functions for QTLretrievR that will be called by the primary functions