# 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

• --keep-ambig

Keep ambiguous SNPs. Only use this option whe base and target has the same A1 and A2 alleles

• --logit-perm

When performing permutation on binary phenotypes, 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

• --no-default

Disable the default options of PRSice.

• --no-full

Do not include the p-value threshold of 1 unless specified in --bar-levels or --upper

• --non-cumulate

Calculate non-cumulative PRS. PRS will be reset to 0 for each new P-value threshold instead ofadding up

• --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 or equal to 10,000

Note

When permutation is required, PRSice will perform the following operation

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
• --print-snp

Print all SNPs used to construct the best PRS

• --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

• --thread | -n

Number of thread use

Tip

Maximum number of thread can be specified by using --thread max

Note

PRSice will limit the maximum number of thread used to the number of core available on the system as detected by PRSice.

• --x-range
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

• --help | -h

Display the help messages