fetchAnalytesInfo: Fetch features of analytes

In DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description

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

Usage

fetchAnalytesInfo(
  oswName,
  maxFdrQuery,
  oswMerged,
  analytes,
  filename,
  runType,
  analyteInGroupLabel = FALSE
)

Arguments

oswName	(char) path to the 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.
oswMerged	(logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
analytes	(vector of strings) transition_group_ids for which features are to be extracted. analyteInGroupLabel must be set according the pattern used here.
filename	(data-frame) Should be from the RUN.FILENAME column from osw files.
runType	(char) This must be one of the strings "DIA_proteomics", "DIA_Metabolomics".
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.

Value

(data-frames) 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.
RT	(numeric) retention time as in FEATURE.EXP_RT of osw files.
delta_rt	(numeric) as in FEATURE.DELTA_RT of osw files.
assay_RT	(numeric) library retention time as in PRECURSOR.LIBRARY_RT of osw files.
Intensity	(numeric) peak intensity as in FEATURE_MS2.AREA_INTENSITY of osw files.
leftWidth	(numeric) as in FEATURE.LEFT_WIDTH of osw files.
rightWidth	(numeric) as in FEATURE.RIGHT_WIDTH 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 <- DIAlignR::getRunNames(dataPath = dataPath)
oswName <- paste0(dataPath,"/osw/merged.osw")
## Not run: 
analytesInfo <- fetchAnalytesInfo(oswName, maxFdrQuery = 0.05, oswMerged = TRUE,
 analytes = c("19051_KLIVTSEGC[160]FK/2"), filename = filenames$filename[2],
  runType = "DIA_proteomics", analyteInGroupLabel = TRUE)
analytesInfo <- fetchAnalytesInfo(oswName, maxFdrQuery = 0.05, oswMerged = TRUE,
 analytes = c("IHFLSPVRPFTLTPGDEEESFIQLITPVR_3"), filename = filenames$filename[3],
  runType = "DIA_proteomics", analyteInGroupLabel = FALSE)

## End(Not run)

DIAlignR documentation built on Nov. 8, 2020, 8:22 p.m.