Sets the metacell dataframe for datasets which are from Proline software

In the quantitative columns, a missing value is identified by no value rather than a value equal to 0.

In these datasets, the metacell info is computed from the 'PSM count' columns.

Conversion rules Initial conversion rules for proline |————–|—————–|—–| | Quanti | PSM count | Tag | |————–|—————–|—–| | == 0 | N.A. | whatever | 2.0 | | > 0 | > 0 | 1.1 | | > 0 | == 0 | 1.2 | | > 0 | unknown col | 1.0 | |————–|—————–|—–|

Usage

Metacell_proline(qdata, conds, df = NULL, level = NULL)

Arguments

qdata

An object of class MsnSet

conds

A 1-col dataframe with the condition associated to each sample.

df

A dataframe with the same dimension as qdata containing the metacell.

level

A string designing the type of entity/pipeline. Available values are: peptide, protein

Value

NA

Author

Samuel Wieczorek

Examples

data(subR25pept)
conds <- design.qf(subR25pept)$Condition
qdata <- SummarizedExperiment::assay(subR25pept[[2]])
df <- Metacell_proline(qdata, conds, level = "peptide")