getOswAnalytes: Fetch analytes from OSW file

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

Description

Get a data-frame of analytes, their chromatogram indices and associated FDR-scores.

Usage

getOswAnalytes(
  fileInfo,
  oswMerged = TRUE,
  analyteInGroupLabel = FALSE,
  maxFdrQuery = 0.05,
  runType = "DIA_Proteomics"
)

Arguments

oswMerged	(logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
analyteInGroupLabel	(logical) TRUE for getting analytes as PRECURSOR.GROUP_LABEL from osw file. FALSE for fetching analytes as PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file.
maxFdrQuery	(numeric) A numeric value between 0 and 1. It is used to filter features from osw file which have SCORE_MS2.QVALUE less than itself.
runType	(char) This must be one of the strings "DIA_Proteomics", "DIA_Metabolomics".
dataPath	(char) path to xics and osw directory.
filenames	(data-frame) column "filename" contains RUN table from osw files. column "runs" contain respective mzML names without extension. To get filenames use getRunNames function.

Value

(A list of data-frames) Each data-frame has following columns:

transition_group_id	(string) it is either fetched from PRECURSOR.GROUP_LABEL or a combination of PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file.
filename	(string) as mentioned in RUN table of osw files.
peak_group_rank	(integer) rank of each feature associated with transition_group_id.
m_score	(numeric) q-value of each feature associated with transition_group_id.
transition_id	(integer) fragment-ion ID associated with transition_group_id. This is matched with chromatogram ID in mzML file.

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-12-13

See Also

getRunNames

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
filenames <- getRunNames(dataPath = dataPath)
## Not run: 
oswFiles <- getOswAnalytes(dataPath = dataPath, filenames = filenames,
 analyteInGroupLabel = TRUE)
oswFiles[["run0"]][1,]
oswFiles <- getOswAnalytes(dataPath = dataPath, filenames = filenames,
 analyteInGroupLabel = FALSE)
oswFiles[["run0"]][1,]

## End(Not run)

Roestlab/DIAlign documentation built on Feb. 25, 2021, 5:18 p.m.