Metacell_proline: Sets the metacell dataframe for datasets which are from...

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

Sets the metacell dataframe for datasets which are from Proline software

Description

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, level = NULL)

Arguments

qdata	An object of class MSnSet
conds	xxx
df	A list of integer xxxxxxx
level	xxx

Value

xxxxx

Author(s)

Samuel Wieczorek

Examples

file <- system.file("extdata", "Exp1_R25_pept.txt", package = "DAPARdata")
data <- read.table(file, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
metadataFile <- system.file("extdata", "samples_Exp1_R25.txt", package = "DAPARdata")
metadata <- read.table(metadataFile, header = TRUE, sep = "\t", as.is = TRUE, stringsAsFactors = FALSE)
conds <- metadata$Condition
qdata <- data[seq_len(100), seq.int(from = 56, to = 61)]
df <- data[seq_len(100), seq.int(from = 43, to = 48)]
df <- Metacell_proline(qdata, conds, df, level = "peptide")

prostarproteomics/DAPAR documentation built on March 28, 2024, 4:44 a.m.