metacombine: Combine peptide metadata to build protein metadata

In prostarproteomics/DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

Combine peptide metadata to build protein metadata

Description

Aggregation rules for the cells metadata of peptides. Please refer to the metacell vocabulary in 'metacell.def()'

# Basic aggregation (RULE 1) Aggregation of a mix of missing values (2.X) with quantitative and/or imputed values (1.X, 3.X) |—————————- Not possible (tag : 'STOP') |—————————-

Aggregation of different types of missing values (among 2.1, 2.2) |—————————- * (RULE 2) Aggregation of 2.1 peptides between each other gives a missing value (2.0) * (RULE 3) Aggregation of 2.2 peptides between each other gives a missing value (2.0) * (RULE 4) Aggregation of a mix of 2.1 and 2.2 gives a missing value (2.0) |—————————-

Aggregation of a mix of quantitative and/or imputed values (among 1.x and 3.X) |—————————- * (RULE 5) if the type of all the peptides to agregate is either 1.0, 1.1 or 1.2, then the final metadata is set to the corresponding tag * (RULE 5bis) if the type of all the peptides to agregate is either 3.0, 3.1 or 3.2, then the final metadata is set to the corresponding tag * (RULE 6) if the set of metacell to agregate is a mix of 1.x, then the final metadata is set to 1.0 * (RULE 7) if the set of metacell to agregate is a mix of 3.x, then the final metadata is set to 3.0 * (RULE 8) if the set of metacell to agregate is a mix of 3.X and 1.X, then the final metadata is set to 4.0

# Post processing Update metacell with POV/MEC status for the categories 2.0 and 3.0 TODO

Usage

metacombine(met, level)

Arguments

met	xxx
level	xxx

Value

xxx

Examples

ll <- metacell.def("peptide")$node
for (i in seq_len(length(ll))) {
  test <- lapply(
    combn(ll, i, simplify = FALSE),
    function(x) tag <- metacombine(x, "peptide")
  )
}

metacombine(c('Quant. by direct id', 'Missing POV'), 'peptide')

prostarproteomics/DAPAR documentation built on Nov. 26, 2024, 6:32 p.m.