MatchSubsequence {atSNP} | R Documentation |
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.
MatchSubsequence(snp.tbl, motif.scores, motif.lib, snpids = NULL, motifs = NULL, ncores = 1)
snp.tbl |
A data.frame with the following information:
| |||||||||||||||||||
motif.scores |
A data.frame with the following information:
| |||||||||||||||||||
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.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. |
Sunyoung Shin sunyoung.shin@utdallas.edu, Chandler Zuo chandler.c.zuo@gmail.com
data(example) MatchSubsequence(motif_scores$snp.tbl, motif_scores$motif.scores, motif_library, ncores=2)