PRSice will automatically generate the bar-plot and high-resolution plot
--fastscore) is not set. Quantile plots will also be generated if
--quantile parameter is provided
To see some example of PRSice output, please refer to here
These parameters, is not recognized by the PRSice binary
Colour of the most predicting threshold. Default:
Colour of the poorest predicting threshold. Default:
When set, will change the colour of bar to p-value threshold instead of the p-value from the association with phenotype
Colour palatte to be used for bar plotting when
--bar_col_p is set. Default:
Plot the top N target phenotypes / gene sets in a summary 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.
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.
Number of quantiles to plot. No quantile plot will be generated when this is not provided.
Parameter to indicate an uneven distribution of quantile. Values represent the upperbound of each quantile group.
--quantile 10 --quant-break 1,5,10, the quantiles will be grouped into
\(0\lt Q \le 1\), \(1\lt Q \le 5\), \(5\lt Q \le 10\)
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.
This will only work if the base and target has a different phenotype or if the target phenotype is quantitative
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
When set, will change the y-axis of the high resolution scatter plot to R2 instead