Description Usage Arguments Value Author(s) Examples
View source: R/motif_analysis.R
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.
1 2 | MatchSubsequence(snp.tbl, motif.scores, motif.lib, snpids = NULL,
motifs = NULL, ncores = 2)
|
snp.tbl |
A data.table with the following information:
| |||||||||||||||||||
motif.scores |
A data.table with the following information:
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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. |
A data.table 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. |
Chandler Zuozuo@stat.wisc.edu
1 2 | data(example)
MatchSubsequence(motif_scores$snp.tbl, motif_scores$motif.scores, motif_library)
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