This function selects the columns necessary for the aLFQ R package.
convert4aLFQ(data, annotation = TRUE, check_transitions = TRUE)A data frame containing the SWATH data in transition-level format
Option to indicate if the data has been annotated, i.e. if the columns Condition, Replicate, Run are present. If option is set to true it will write a new run_id as a string of the combination of these three columns.
Option if number of transitions should be checked. As input only transition-level data should be used and therefore this is checked. However, this makes the function slow and herewith be omitted.
Returns a data frame in the appropriate format for aLFQ.
{
data("OpenSWATH_data", package="SWATH2stats")
data("Study_design", package="SWATH2stats")
data <- SWATH2stats::sample_annotation(OpenSWATH_data, Study_design, verbose=TRUE)
data.filtered.decoy <- filter_mscore(data, 0.01)
raw <- disaggregate(data.filtered.decoy)
data.aLFQ <- convert4aLFQ(raw)
}
#> peterb_J131223_043
#> peterb_J131223_054
#> peterb_L150425_003b_SW
#> peterb_L150425_011_SW
#> peterb_L150514_001_SW
#> peterb_L150514_002_SW
#> Dimension difference: 931, 0
#> The library contains 6 transitions per precursor.
#>
#> The data table was transformed into a table containing one row per transition.
#> Checking the integrity of the transitions takes a lot of time.
#> To speed up consider changing the option.