ComputePValues {atSNP} | R Documentation |
This function computes the p-values for allele-specific affinity scores and between-allele affinity score changes using the importance sampling technique.
ComputePValues(motif.lib, snp.info, motif.scores, ncores = 1, testing.mc = FALSE, figdir = NULL)
motif.lib |
A list object with the output format of function
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snp.info |
A list object with the output format of function
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motif.scores |
A data.frame object containing at least the following columns:
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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). |
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. |
Sunyoung Shin sunyoung.shin@utdallas.edu, Chandler Zuo chandler.c.zuo@gmail.com
data(example) ComputePValues(motif_library, snpInfo, motif_scores$motif.scores, ncores = 2, testing.mc=TRUE)