Skip to contents

Get Traits in Clerc et al. 2018

traits_clerc_2018.Rd

These traits are the ones used by Clerc et al. 2018 (https://doi.org/10.1053/j.gastro.2018.05.030). We generally don't recommend using these traits because they are either redundant or missing some important traits. We include this function because this paper is very influential in the field.

Usage

traits_clerc_2018(sia_link = FALSE)

Arguments

A boolean indicating whether to include sialic acid linkage traits. Default is FALSE.

Value

A named list of derived traits.

Usage of sialic acid linkage traits

To use these sialic acid linkage traits, var_info of the input glyexp::experiment() must have the following columns:

  • nE: Number of a2,6-linked sialic acids

  • nL: Number of a2,3-linked sialic acids

Note that you have to add these two columns even if the glycan_structure column has intact linkages. This is because by convention all traits work with glycan structures with "basic" structure levels (i.e., with generic monosaccharides like "Hex" and "HexNAc" and no linkages specified).

Examples

traits_clerc_2018()[1:5]
#> $CA1
#> prop(nA == 1, na_action = "keep")
#> 
#> $CA2
#> prop(nA == 2, na_action = "keep")
#> 
#> $CA3
#> prop(nA == 3, na_action = "keep")
#> 
#> $CA4
#> prop(nA == 4, na_action = "keep")
#> 
#> $TC
#> prop(Tp == "complex", na_action = "keep")
#>