Introduction

PRSice will automatically generate the bar-plot and high-resolution plot (if --fastscore) is not set. Quantile plots will also be generated if the --quantile parameter is provided

To see some example of PRSice output, please refer to here

Note

These parameters, is not recognized by the PRSice binary

Command

  • --bar-col-high

Colour of the most predicting threshold. Default: firebrick

  • --bar-col-lower

Colour of the poorest predicting threshold. Default: dodgerblue

  • --bar-col-p

When set, will change the colour of bar to p-value threshold instead of the p-value from the association with phenotype

  • --bar-palatte

Colour palatte to be used for bar plotting when --bar_col_p is set. Default: YlOrRd

  • --multi-plot

Plot the top N target phenotypes / gene sets in a summary plot

  • --plot

When set, will only perform plotting using existing PRSice result files. All other parameters are still required such that PRSice can correctly locate the required input files for plotting.

  • --plot-set

The default behaviour of PRSet is to plot the bar-chart, high-resolution plot and quantile plot of the "Base" gene set, which consider all SNPs within the genome. By using the --plot-set option, you can plot the specific set of interest.

  • --quantile | -q

    Number of quantiles to plot. No quantile plot will be generated when this is not provided.

  • --quant-break

    Parameter to indicate an uneven distribution of quantile. Values represent the upperbound of each quantile group.

    e.g. With --quantile 10 --quant-break 1,5,10, the quantiles will be grouped into

    \(0\lt Q \le 1\), \(1\lt Q \le 5\), \(5\lt Q \le 10\)

  • --quant-extract | -e

File containing sample ID to be plot on a separated quantile e.g. extra quantile containing only schizophrenia samples. Must contain IID. Should contain FID if --ignore-fid isn't set.

Note

This will only work if the base and target has a different phenotype or if the target phenotype is quantitative

  • --quant-ref

Reference quantile for quantile plot. Default is number of quantiles divided by 2

Or in the event where --quant-break is used, represent the upper bound of the reference quantile

  • --scatter-r2

When set, will change the y-axis of the high resolution scatter plot to R2 instead