fetchAnalytesInfo: Fetch features of analytes

View source: R/read_osw.R

fetchAnalytesInfoR Documentation

Fetch features of analytes

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 = "DIA_Proteomics",
  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, shubh.gupta@mail.utoronto.ca

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)
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)

shubham1637/DIAlign documentation built on Jan. 28, 2023, 1:22 a.m.