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Get Basic Derived Traits

basic_traits.Rd

These derived traits are the most basic and commonly used derived traits. They describe global properties of a glycome including the type of glycans, fucosylation level, sialylation level, galactosylation level, and branching level.

Usage

basic_traits()

Value

A named list of derived traits.

Details

The explanations of the derived traits are as follows:

  • TM: Proportion of highmannose glycans

  • TH: Proportion of hybrid glycans

  • TC: Proportion of complex glycans

  • MM: Average number of mannoses within highmannose glycans

  • CA2: Proportion of bi-antennary glycans within complex glycans

  • CA3: Proportion of tri-antennary glycans within complex glycans

  • CA4: Proportion of tetra-antennary glycans within complex glycans

  • TF: Proportion of fucosylated glycans

  • TFc: Proportion of core-fucosylated glycans

  • TFa: Proportion of arm-fucosylated glycans

  • TB: Proportion of glycans with bisecting GlcNAc

  • SG: Average degree of sialylation per galactose

  • GA: Average degree of galactosylation per antenna

  • TS: Proportion of sialylated glycans

Examples

basic_traits()
#> $TM
#> prop(Tp == "highmannose", na_action = "keep")
#> 
#> $TH
#> prop(Tp == "hybrid", na_action = "keep")
#> 
#> $TC
#> prop(Tp == "complex", na_action = "keep")
#> 
#> $MM
#> wmean(nM, within = (Tp == "highmannose"), na_action = "keep")
#> 
#> $CA2
#> prop(nA == 2, within = (Tp == "complex"), na_action = "keep")
#> 
#> $CA3
#> prop(nA == 3, within = (Tp == "complex"), na_action = "keep")
#> 
#> $CA4
#> prop(nA == 4, within = (Tp == "complex"), na_action = "keep")
#> 
#> $TF
#> prop(nF > 0, na_action = "keep")
#> 
#> $TFc
#> prop(nFc > 0, na_action = "keep")
#> 
#> $TFa
#> prop(nFa > 0, na_action = "keep")
#> 
#> $TB
#> prop(B, na_action = "keep")
#> 
#> $SG
#> wmean(nS/nG, na_action = "keep")
#> 
#> $GA
#> wmean(nG/nA, na_action = "keep")
#> 
#> $TS
#> prop(nS > 0, na_action = "keep")
#>