ComputePValues {atSNP} | R Documentation

## Compute p-values for affinity scores.

### Description

This function computes the p-values for allele-specific affinity scores and between-allele affinity score changes using the importance sampling technique.

### Usage

    ComputePValues(motif.lib, snp.info, motif.scores, ncores = 1,
      testing.mc = FALSE, figdir = NULL)

### Arguments

`motif.lib` | A list object with the output format of function `LoadMotifLibrary`.
`snp.info` | A list object with the output format of function `LoadSNPData`.
`motif.scores` | A data.frame object containing at least the following columns:
motif | The name of the motif.
log_lik_ref | The log-likelihood score for the reference allele.
log_lik_snp | The log-likelihood score for the SNP allele.
`ncores` | An integer for the number of parallel process. Default: 1.
`testing.mc` | Monte Carlo sample size of 200 is considered. Do not change the default unless conducting a quick test. Default: FALSE
`figdir` | A string for the path to print p-value plots for monitoring results. Default: NULL (no figure).

### Value

A data.frame extending `motif.scores` by the following additional columns:

pval_ref | P-values for scores on the reference allele.
pval_snp | P-values for scores on the SNP allele.
pval_cond_ref | Conditional p-values for scores on the reference allele.
pval_cond_snp | Conditional p-values for scores on the SNP allele.
pval_diff | P-values for the difference in scores between the reference and the SNP alleles.
pval_rank | P-values for the log rank ratio between the reference and the SNP alleles.

### Author(s)

Sunyoung Shin sunyoung.shin@utdallas.edu, Chandler Zuo chandler.c.zuo@gmail.com

### Examples

    data(example)
    ComputePValues(motif_library, snpInfo, motif_scores$motif.scores, ncores = 2, testing.mc=TRUE)

[Package atSNP version 1.2.0 Index]