FSWE.initConfiguration: FSWE.initConfiguration

In IFIproteomics/LFQbench: Label Free Quantitation benchmark package

FSWE.initConfiguration

Description

define software list and the list of initialization function for each software

Usage

FSWE.initConfiguration(injectionNames, speciesTags)

Arguments

injectionNames

: a data frame the injection names of each experiment considered. You may process several experiments together (each experiment is a column of the data frame. The row names of the data frame are used as column names in the FSWE output.). Example: dataSets = data.frame( "TTOF5600_32w"=c("lgillet_L150206_001", "lgillet_L150206_003", "lgillet_L150206_005", "lgillet_L150206_002", "lgillet_L150206_013", "lgillet_L150206_014"), ,"TTOF5600_64w"=c("lgillet_L150206_007", "lgillet_L150206_009", "lgillet_L150206_011", "lgillet_L150206_008", "lgillet_L150206_010", "lgillet_L150206_012") ,"TTOF6600_32w"=c("lgillet_I150211_002", "lgillet_I150211_004", "lgillet_I150211_006", "lgillet_I150211_003", "lgillet_I150211_005", "lgillet_I150211_007") ,"TTOF6600x64w"=c("lgillet_I150211_008", "lgillet_I150211_010", "lgillet_I150211_012", "lgillet_I150211_009", "lgillet_I150211_011", "lgillet_I150211_013") ,row.names=c("A1", "A2", "A3", "B1", "B2", "B3"))

speciesTags

: Namesa named vector containing tags to locate the corresponding species at the protein name reported by the software. In SwissProt you may use something like _SPECIES. Names of elements must contain all LFQbench.Config$AllSpecies Example: speciesTags = list(HUMAN = "_HUMAN", YEAST = "_YEAS", ECOLI = "_ECOLI")

IFIproteomics/LFQbench documentation built on March 2, 2023, 9:45 a.m.