plotMotifMatch: Plot sequence logos of the position weight matrix of the...

In kinsigne/atSNP_modified: Affinity test for identifying regulatory SNPs.

Description

Plot the best matching augmented subsequences on the reference and SNP alleles. Plot sequence logos of the position weight matrix of the motif to the corresponding positions of the best matching subsequences on the references and SNP alleles.

Usage

plotMotifMatch(snp.tbl, motif.scores, snpid, motif, motif.lib, cex.main = 2,
  ...)

Arguments

snp.tbl	A data.table 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.table 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.
snpid	A snpid to plot the sequences on the reference and SNP alleles
motif	A motif to match the sequences with its position weight matrix
motif.lib	A list of position weight matrices
cex.main	The size of the main title.
...	Other parameters passed to plotMotifLogo.

Value

Sequence logo stacks: Reference subsequences, sequence logo of reference allele matching potision weight matrix, SNP subsequences, sequence logo of SNP allele matching potision weight matrix

Author(s)

Sunyoung [e-mail]

Examples

data(example)
plotMotifMatch(motif_scores$snp.tbl, motif_scores$motif.scores, motif_scores$snp.tbl$snpid[1], motif_scores$motif.scores$motif[1], motif.lib = motif_library)

kinsigne/atSNP_modified documentation built on May 23, 2019, 4:24 p.m.