# Introduction¶

Below are some other parameters available for PRSice

# Command¶

• --all-score Output PRS for ALL threshold. !!! warning This will generate a huge file

• --exclude

File contains SNPs to be excluded from the analysis. Mutually exclusive from --extract

• --extract

File contains SNPs to be included in the analysis. Mutually exclusive from --exclude

• --ignore-fid

Ignore FID for all input. When this is set, first column of all file will be assume to be IID instead of FID

• --logit-perm

When performing permutation, still use logistic regression instead of linear regression. This will substantially slow down PRSice.

Note

One problem with using --logit-perm is 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-perm option. In most case, the p-value of the linear model should be similar to the logistic model

• --keep-ambig

Keep ambiguous SNPs. Only use this option if you are certain that the base and target has the same A1 and A2 alleles

• --out | -o

Prefix for all file output.

Note

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))

• --perm

Number of permutation to perform. This will generate the empirical p-value. Recommend to use value larger than 10,000

Note

Essentially, when permutation is required, PRSice will perform the following operation (with slight difference in implementation for optimum performance)

1. Perform normal PRSice across all thresholds and obtain p-value of the most significant threshold
2. 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
• --seed | -s

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

• --print-snp

Print all SNPs used to construct the best PRS

• --thread | -n

You can ask for maximum number of thread by using --thread max
• --help | -h