consensus: Consensus sequence determination
In BALCONY: Better ALignment CONsensus analYsis

Description Usage Arguments Details Value Note Author(s) See Also Examples

Function calculates consensus sequence for given alignment with a threshold of user's choice.

1	consensus(alignment, threshold)

`alignment`	output of of `read.alignment` function or grouped alignment created with: `align_seq_mtx2grs` and `alignment2matrix`
`threshold`	minimal fraction of amino acids on the certain position in all sequences of the alignment to be taken for consensus letter on this position; number in range 0-100.

If maximum fraction of any amino acid on the certain position is lower than a threshold then "*" is printed instead.

consensus_sequence

A character vector of length of the aligned sequence containing consesus sequence based on the input alignment

Please note that this function masks the seqinr package function consensus

Alicja Pluciennik & Michal Stolarczyk

s2c

data("alignment")
alignment = delete_isoforms(alignment)
threshold=80 # Set the consensus threshold
consensus_sequence=consensus(alignment, threshold)

Loading required package: seqinr
Loading required package: Rpdb
Loading required package: rgl

Attaching package: 'Rpdb'

The following objects are masked from 'package:base':

    norm, replicate, unsplit

Loading required package: scales

Attaching package: 'BALCONY'

The following object is masked from 'package:seqinr':

    consensus

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found