Below are some other parameters available for PRSice
Output PRS for ALL threshold.
This will generate a huge file
File contains SNPs to be excluded from the analysis. Mutually exclusive from
File contains SNPs to be included in the analysis. Mutually exclusive from
Ignore FID for all input. When this is set, first column of all file will be assume to be IID instead of FID
Keep ambiguous SNPs. Only use this option whe base and target has the same A1 and A2 alleles
When performing permutation on binary phenotypes, use logistic regression instead of linear regression. This will substantially slow down PRSice.
One problem with using
--logit-permis that some of the permuted phenotype might be suffer from perfect separation. This leads to the GLM logistic model not being able to be converge (thus terminating PRSice).
If you encounter such problem, you might want to exclude the
--logit-permoption. In most case, the p-value of the linear model should be similar to the logistic model
Disable the default options of PRSice.
Do not include the p-value threshold of 1 unless specified in
Calculate non-cumulative PRS. PRS will be reset to 0 for each new P-value threshold instead ofadding up
Prefix for all file output.
If multiple target phenotypes are included (e.g. using
--pheno-col), the phenotype will be appended to the output prefix
If multiple gene set are included, the name of the set will be appended to the output prefix (after the phenotype (if any))
Number of permutation to perform. This will generate the empirical p-value. Recommend to use value larger than or equal to 10,000
When permutation is required, PRSice will perform the following operation
- Perform normal PRSice across all thresholds and obtain p-value of the most significant threshold
- Repeat PRSice analysis N times with permuted phenotype. Count the number of time where the p-value of the most significant threshold for the permuted
Print all SNPs used to construct the best PRS
Seed used for permutation. If not provided, system time will be used as seed. This will allow the same results to be generated when the same seed and input is used
Number of thread use
Maximum number of thread can be specified by using
PRSice will limit the maximum number of thread used to the number of core available on the system as detected by PRSice.
Range of SNPs to be excluded from the whole analysis. It can either be a single bed file or a comma seperated list of range. Range must be in the format of chr:start-end or chr:coordinate
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