set_frame: Take an input sequence and get it into the reading frame....

View source: R/frame_seq.r

set_frameR Documentation

Take an input sequence and get it into the reading frame. Uses the path of the sequence through the PHMM to located the first long contigious stretch of 1s (matches) Note - there is an imbalance in operation, namely the function checks for a run of 10 additional 1s on the front of the sequence, and for a run of only 3 additional matches on the back. The front of the sequence is high priority because it is necessary to ensure the sequence is in frame. whereas matching on the back is more lenient as insertions and deletions can be tolerated here without large implications for the rest of the sequence

Description

Take an input sequence and get it into the reading frame. Uses the path of the sequence through the PHMM to located the first long contigious stretch of 1s (matches) Note - there is an imbalance in operation, namely the function checks for a run of 10 additional 1s on the front of the sequence, and for a run of only 3 additional matches on the back. The front of the sequence is high priority because it is necessary to ensure the sequence is in frame. whereas matching on the back is more lenient as insertions and deletions can be tolerated here without large implications for the rest of the sequence

Usage

set_frame(org_seq_vec, path_out)

debar documentation built on May 29, 2024, 2:02 a.m.