dtMotifMatch: Compute the augmented matching subsequence on SNP and...

In chandlerzuo/atSNP: Affinity test for identifying regulatory SNPs

Description

Calculate the best matching augmented subsequences on both SNP and reference alleles for motifs. Obtain extra unmatching position on the best matching augmented subsequence of the reference and SNP alleles.

Usage

dtMotifMatch(
  snp.tbl,
  motif.scores,
  snpids = NULL,
  motifs = NULL,
  motif.lib,
  ncores = 2
)

Arguments

snp.tbl	A data.frame with the following information: snpid SNP id. ref_seq Reference allele nucleobase sequence. snp_seq SNP allele nucleobase sequence. ref_seq_rev Reference allele nucleobase sequence on the reverse strand. snp_seq_rev SNP allele nucleobase 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.
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.
motif.lib	A list of named position weight matrices.
ncores	The number of cores used for parallel computing. Default: 10

Value

A data.frame containing all columns from the function, MatchSubsequence. In addition, the following columns are added:

snp_ref_start, snp_ref_end, snp_ref_length	Location and Length of the best matching augmented subsequence on both the reference and SNP allele.
ref_aug_match_seq_forward	Best matching augmented subsequence or its corresponding sequence to the forward strand on the reference allele.
snp_aug_match_seq_forward	Best matching augmented subsequence or its corresponding sequence to the forward strand on the SNP allele.
ref_aug_match_seq_reverse	Best matching augmented subsequence or its corresponding sequence to the reverse strand on the reference allele.
snp_aug_match_seq_reverse	Best matching augmented subsequence or its corresponding sequence to the reverse strand on the SNP allele.
ref_location	SNP location of the best matching augmented subsequence on the reference allele. Starting from zero.
snp_location	SNP location of the best matching augmented subsequence on the SNP allele. Starting from zero.
ref_extra_pwm_left	Left extra unmatching position on the best matching augmented subsequence of the reference allele.
ref_extra_pwm_right	Right extra unmatching position on the best matching augmented subsequence of the reference allele.
snp_extra_pwm_left	Left extra unmatching position on the best matching augmented subsequence of the SNP allele.
snp_extra_pwm_right	Right extra unmatching position on the best matching augmented subsequence of the SNP allele.

Author(s)

Sunyoung [e-mail]

Examples

data(example)
dtMotifMatch(motif_scores$snp.tbl, motif_scores$motif.scores,
motif.lib = motif_library)

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