Step: Quantify Motifs

Quantify glycan motifs using glydet::quantify_motifs(). The motifs are extracted using glymotif::extract_branch_motif() for N-glycans and glymotif::extract_motif() for others. Advanced glycan motif analysis that quantify glycan motifs (substructures) of a glycome or each glycosite. Need glycan structure information.

Usage

step_quantify_motifs(max_size = 3, method = "relative")

Arguments

max_size

Maximum size of motifs to extract.

method

Method for motif quantification ("relative" or "absolute").

Value

A glysmith_step object.

Details

Data required:

• exp: The experiment to quantify motifs for

Data generated:

• motif_exp: The experiment with quantified motifs

Tables generated:

• quantified_motifs: A table containing the quantified motifs.

AI Prompt

This section is for AI in inquire_blueprint() only.

• Include this step if needed.

• This step should be followed by the DEA step and visualization steps.

See also

glydet::quantify_motifs(), glymotif::extract_motif(), glymotif::extract_branch_motif()

Examples

step_quantify_motifs()
#> <step "step_quantify_motifs()"> Motif quantification