analytesFromFeatures: Outputs analytes below FDR

In Roestlab/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description

Provides all found analytes or only common analytes that have m-score less than analyteFDR.

Usage

analytesFromFeatures(features, analyteFDR = 1, commonAnalytes = TRUE)

Arguments

features	(list of data-frames) contains features and their properties identified in each run.
analyteFDR	(numeric) only analytes that have m-score less than this, will be included in the output.
commonAnalytes	(logical) TRUE: intersect across all runs, FASLE: union across all runs.

Value

a vector of integer.

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-04-14

See Also

getFeatures

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
fileInfo <- getRunNames(dataPath = dataPath)
features <- getFeatures(fileInfo, maxFdrQuery = 1.00, runType = "DIA_Proteomics")
## Not run: 
commonAnalytes <- analytesFromFeatures(features, analyteFDR = 0.01, commonAnalytes = TRUE)

## End(Not run)

Roestlab/DIAlignR documentation built on March 3, 2021, 9:09 a.m.