MatchSubsequence: Compute the matching subsequence.

In chandlerzuo/atSNP: Affinity test for identifying regulatory SNPs

Description

This function combines the SNP set, the motif library and the affinity score table and produce the matching subsequence found at each SNP location for each motif.

Usage

MatchSubsequence(
  snp.tbl,
  motif.scores,
  motif.lib,
  snpids = NULL,
  motifs = NULL,
  ncores = 1
)

Arguments

snp.tbl	A data.frame with the following information: snpid SNP id. ref_seq Reference allele nucleotide sequence. snp_seq SNP allele nucleotide sequence. ref_seq_rev Reference allele nucleotide sequence on the reverse strand. snp_seq_rev SNP allele nucleotide sequence on the reverse strand.
motif.scores	A data.frame with the following information: motif Name of the motif. motif_len Length of the motif. ref_start, ref_end, ref_strand Location of the best matching subsequence on the reference allele. snp_start, snp_end, snp_strand Location of the best matching subsequence on the SNP allele. log_lik_ref Log-likelihood score for the reference allele. log_lik_snp Log-likelihood score for the SNP allele. log_lik_ratio The log-likelihood ratio. log_enhance_odds Difference in log-likelihood ratio between SNP allele and reference allele based on the best matching subsequence on the reference allele. log_reduce_odds Difference in log-likelihood ratio between reference allele and SNP allele based on the best matching subsequence on the SNP allele.
motif.lib	A list of the position weight matrices for the motifs.
snpids	A subset of snpids to compute the subsequences. Default: NULL, when all snps are computed.
motifs	A subset of motifs to compute the subsequences. Default: NULL, when all motifs are computed.
ncores	The number of cores used for parallel computing.

Value

A data.frame containing all columns in both snp.tbl and motif.scores. In addition, the following columns are added:

ref_match_seq	Best matching subsequence on the reference allele.
snp_match_seq	Best matching subsequence on the SNP allele.
ref_seq_snp_match	Subsequence on the reference allele corresponding to the best matching location on the SNP allele.
snp_seq_ref_match	Subsequence on the SNP allele corresponding to the best matching location on the reference allele.

Author(s)

Sunyoung Shin [e-mail], Chandler Zuo [e-mail]

Examples

data(example)
MatchSubsequence(motif_scores$snp.tbl, motif_scores$motif.scores,
motif_library, ncores=2)

chandlerzuo/atSNP documentation built on Oct. 31, 2020, 4:33 a.m.