Bioinformatics

Alignment metrics operator

Description

alignment_metrics operator returns some metrics summarising a multiple sequence alignment.

Usage
Input projection .
row numeric, input data, per cell
col numeric, input data, per cell
colors numeric, input data, per cell
y-axis numeric, input data, per cell
Properties .
sequence_type factor, sequence type (protein, dna, rna)
substitution_matrix factor, substitution amtrix (default: BLOSUM62)
gap_vs_gap factor, gap vs gap score (default: NA)
Output relations .
conservation_score numeric, conservation score at each position (column)
n_gaps numeric, number of gaps at each position (column)
gap_proportion numeric, conservation score at each position (column)

Pairwise sequence distance operator

Description

dist_alignment computes pairwise distances between aligned biological sequences.

Usage
Input projection .
row factor, sequence names/IDs
col numeric, position
y-axis numeric, value corresponding to amino or nucleic acid
color factor, optional, letter
Properties .
sequence_type whether it is dna, rna, or protein sequences
matrix the matrix distance to be used, can be “similarity” or “identity”
gap with nucleotides, if set to 1, gaps will be counted in the identity measure
Output relations .
dist_to numeric, sequence name
dist numeric, distance
Details

This operator compute a matrix of pairwise distances from aligned sequences using similarity (Fitch matrix, for protein sequences only) or identity matrix (for protein and DNA sequences). The resulting matrix contains the squared root of the pairwise distances. For example, if identity between 2 sequences is 80 the squared root of (1.0 - 0.8) i.e. 0.4472136.

Gene Set Enrichment Analysis operator

Description

gsea operator performs a Gene Set Enrichment Analysis (GSEA).

Usage
Input projection .
y-axis numeric, measurement (e.g. normalized gene expression value)
row factor, gene set
col factor, gene name
Properties .
min_size numeric, minimal size of a gene set to be considered in the analysis (default: 10)
max_size numeric, maximal size of a gene set to be considered in the analysis (default: 500)
n_perm numeric, number of permutations (default: 1000)
Output relations .
pval numeric, p-value of the test
padj numeric, adjusted p-value of the test
ES numeric, enrichment score
NES numeric, normalised enrichment score
Details
References

This operator is a wrapper of the fgsea function from the fgsea R/Bioconductor package.

See GSEA on Wikipedia.

Multiple Sequence Alignment operator

Description

msa operator performs Multiple Sequence Alignment.

Usage
Input projection .
row factor, sequence names/IDs
col numeric, position
y-axis numeric, value corresponding to amino or nucleic acid
color factor, optional, letter
Properties .
sequence_type whether it is dna, rna, or protein sequences
method alignment method, can be ClustalW, Muscle, DECIPHER, or ClustalOmega
Output relations .
aligned_position numeric, position in the alignment
Details

The operator uses the Clustal algorithm with default parameters.

MSA Shiny operator

Description

The MSA Shiny operator allows one to create an interactive visualisation fo a Multiple Sequence Alignment.

Usage
Input projection .
row character, aligned sequences
row character, sequence names
Output relations .
Operator view view of the Shiny application

Read FASTA operator

Description

read_fasta operator reads a FASTA file into Tercen.

Usage
Input projection .
col factor, document ID
Output relations .
name factor, sequence name
position numeric, position of amino or nucleic acid in the sequence
letter factor, letter corresponding to an amino or nucleic acid
value numeric, numeric value associated to an amino or nucleic acid
Details

This opeartor reads a FASTA file and returns a table with one row per sequence per letter. Columns correspond to the sequence name (extracted from identifier lines starting with >), position on the sequence (starting from 1 at the beginning of the sequence), the letter (corresponding to an amino or nucleic acid), and a value (corresponding to a numeric encoding of letters for visualisation purposes).

See Also

msa_operator

Sequence to table operator

Description

seq2table Converts a biological sequence to a tabular format.

Usage
Input projection .
row character, sequences to convert
Output relations .
letter character, letter (amino or nucleic acid)
position numeric, position in the sequence
presence boolean, presence of a letter (if 0, gap in the alignment corresponding to a “-” character in the sequence)
Details
References
See Also
Examples