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Create a Proportion Trait

prop.Rd

A proportion trait is the proportion of certain group of glycans within a larger group of glycans. For example, the proportion of sialylated glycans within all glycans, or the proportion of tetra-antennary glycans within all complex glycans. This type of traits is the most common type of glycan derived traits. It can be regarded as a special case of the ratio trait (see ratio()).

Usage

prop(cond, within = NULL, na_action = "keep")

Arguments

cond

Condition to use for defining the smaller group. An expression that evaluates to a logical vector. The names of all built-in meta-properties (see all_mp_fns()) and custom meta-properties can be used in the expression.

within

Condition to use for defining the larger group, with the same format as cond. If NULL (default), all glycans are used as the larger group.

na_action

How to handle missing values.

  • "keep" (default): keep the missing values as NA.

  • "zero": set the missing values to 0.

Value

A derived trait function.

How to use

You can use prop() to create proportion trait easily.

For example:

# Proportion of core-fucosylated glycans within all glycans
prop(nFc > 0)

# Proportion of complex glycans within all glycans
prop(Tp == "complex")

# Proportion of sialylated and fucosylated glycans within all glycans
prop(nS > 0 & nFc > 0)

Note that the last example uses & for logical AND. Actually, you can use any logical operator in the expression in R (e.g., |, !, etc.).

If you want to perform a pre-filtering before calculating the proportion, for example, you want to calculate the proportion of core-fucosylated glycans within only complex glycans, you can use within to define the denominator.

# Proportion of core-fucosylated glycans within complex glycans
prop(nFc > 0, within = (Tp == "complex"))

# Proportion of core-fucosylated glycans with tetra-antenary complex glycans
prop(nFc > 0, within = (Tp == "complex" & nA == 4))

The parentheses around the condition in within are optional, but it is recommended to use them for clarity.

Note about NA

All the internal summation operations ignore NAs by default. Therefore, NAs in the expression matrix and meta-property values will not result in NAs in the derived traits. However, as all derived traits calculate a ratio of two values, NAs will be introduced when:

  1. The denominator is 0. This can happen when the within condition selects no glycans.

  2. Both the numerator and denominator are 0.

Examples

# Proportion of core-fucosylated glycans within all glycans
prop(nFc > 0)
#> prop(nFc > 0, na_action = "keep")

# Proportion of bisecting glycans within all glycans
prop(B)
#> prop(B, na_action = "keep")

# Proportion of sialylated and arm-fucosylated glycans within all glycans
prop(nS > 0 & nFa > 0)
#> prop(nS > 0 & nFa > 0, na_action = "keep")

# Proportion of bi-antennary glycans within complex glycans
prop(nA == 2, within = (Tp == "complex"))
#> prop(nA == 2, within = (Tp == "complex"), na_action = "keep")

# Proportion of sialylated glycans within core-fucosylated tetra-antennary glycans
prop(nS > 0, within = (nFc > 0 & nA == 4))
#> prop(nS > 0, within = (nFc > 0 & nA == 4), na_action = "keep")