getRefPosition: Determine the reference position in a multiple sequence...

Description Usage Arguments Value

Description

Typically, one will call plotMSA to view a variant call in an alignment, but that function takes coordinates in terms of alignment positions, not reference genome positions. This function converts a reference genome location to an alignment location. It does this by taking the start of the alignment on the genome, and then figures out how much further it needs to go to get the respective genome position in the alignment.

Usage

1
getRefPosition(tstart, pos, df)

Arguments

tstart

The initial position of the alignment.

pos

The

df

Data frame returned by AlnsToDataFrame. The seq in the

fasta_name

Full path of the fasta file used to generate the CCS alignment

Value

Returns The genome position


PacificBiosciences/ccsviewr documentation built on May 7, 2019, 11:55 p.m.