Description Usage Arguments Value Examples
View source: R/searchHashTable.R
Searches hash table obtained using the buildHashTable function for occurences of query sequences from FASTA file.
1 2 | searchHashTable(querySequences, hashTable, k = 10, results = 1,
tolerance = 1)
|
querySequences |
FASTA file containing sequences we are searching for |
hashTable |
output of buildHashTable function |
k |
number of bases the query sequences are divided into, must be the same as in buildHashTable |
results |
number of top results of the SSAHA method that will be provie in the outpus list |
tolerance |
tolerance for insertions and deletions in number of nucleotides |
A list of matrices containg best matches and score for each query sequence.
1 | searchHashTable("query.fasta", hashTable, k=10, results = 10, tolerance = 5)
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