| Type: | Package |
| Title: | Nominal Peak Analysis (NPA) |
| Version: | 1.2 |
| Depends: | R (≥ 4.0) |
| Imports: | IDSL.MXP, IDSL.IPA, IDSL.FSA, readxl |
| Author: | Sadjad Fakouri-Baygi
 [aut],
Dinesh Barupal
[cre, aut] |
| Maintainer: | Dinesh Barupal <dinesh.barupal@mssm.edu> |
| Description: | A pipeline to process nominal mass spectrometry data to create .msp files for untargeted analyses. |
| License: | MIT + file LICENSE |
| URL: | https://github.com/idslme/idsl.npa |
| BugReports: | https://github.com/idslme/idsl.npa/issues |
| Encoding: | UTF-8 |
| Archs: | i386, x64 |
| NeedsCompilation: | no |
| Packaged: | 2023-06-27 21:43:10 UTC; sfbaygi |
| Repository: | CRAN |
| Date/Publication: | 2023-06-29 14:00:05 UTC |
IDSL.NPA MSP Generator
Description
This function creates standard .msp files that can also be used for Pepsearch.
Usage
IDSL.NPA_MSPgenerator(NPA_peaklist, number_processing_threads = 1)
Arguments
NPA_peaklist |
A dataframe peaklist of co-detected peaks |
number_processing_threads |
Number of processing threads for multi-threaded processing |
Value
A string of standard .msp file
IDSL.NPA Reference MSP Generator
Description
This function creates reference standard .msp files.
Usage
IDSL.NPA_referenceMSPgenerator(NPA_peaklist, refNPAtable, selectedPeaks_IDref)
Arguments
NPA_peaklist |
A dataframe peaklist of co-detected peaks |
refNPAtable |
reference NPA table |
selectedPeaks_IDref |
selectedPeaks_IDref |
Value
A string of standard .msp file
IDSL.NPA workflow
Description
This function executes the NPA workflow.
Usage
IDSL.NPA_workflow(spreadsheet)
Arguments
spreadsheet |
NPA spreadsheet |
Value
This function organizes the IDSL.NPA file processing for better performance using the template spreadsheet.
IDSL.NPA workflow xlsx Analyzer
Description
This function processes the spreadsheet of the NPA parameters to ensure the parameter inputs are consistent with the requirements of the IDSL.NPA pipeline.
Usage
IDSL.NPA_xlsxAnalyzer(spreadsheet)
Arguments
spreadsheet |
'Start' tab of the parameter spreadsheet |
Value
This function returns the NPA parameters to feed the 'IDSL.NPA_workflow' function.
NPA Fragmentation Peaks Detection
Description
This function detects fragmentation peaks for the NPA analysis
Usage
NPA_fragmentationPeakDetection(input_MS_path, MSfilename, smoothingWindow,
peakHeightThreshold, minSNRbaseline, RTtolerance, nSpline, topRatioPeakHeight,
minIonRangeDifference, minNumNPApeaks, pearsonRHOthreshold, outputNPAeic = NULL,
number_processing_threads = 1)
Arguments
input_MS_path |
path to the MS files |
MSfilename |
MS file |
smoothingWindow |
number of scans for peak smoothing. |
peakHeightThreshold |
A minimum peak height threshold |
minSNRbaseline |
A minimum baseline S/N threshold |
RTtolerance |
retention time tolerance to detect common peaks |
nSpline |
number of points for further smoothing using a cubic spline smoothing method to add more points to calculate Pearson correlation rho values |
topRatioPeakHeight |
The top percentage of the chromatographic peak to calculate Pearson correlation rho values |
minIonRangeDifference |
Minimum distance (Da) between lowest and highest m/z to prevent clustering isotopic envelopes |
minNumNPApeaks |
Minumum number of ions in a NPA cluster |
pearsonRHOthreshold |
Minimum threshold for Pearson correlation rho values |
outputNPAeic |
When 'NULL' NPA EICs are not plotted. 'outputNPAeic' represents an address to save NPA EICs figures. |
number_processing_threads |
Number of processing threads for multi-threaded processing |
Value
A dataframe peaklist of co-detected NPA analysis.
NPA Peak Deconvolution
Description
This function detects fragmentation peaks for the NPA analysis.
Usage
NPA_peakDeconvolution(input_MS_path, MSfilename, smoothingWindow,
peakHeightThreshold, minSNRbaseline, number_processing_threads = 1)
Arguments
input_MS_path |
path to the MS files |
MSfilename |
MS file |
smoothingWindow |
number of scans for peak smoothing. |
peakHeightThreshold |
A minimum peak height threshold |
minSNRbaseline |
A minimum baseline S/N threshold |
number_processing_threads |
Number of processing threads for multi-threaded processing |
Value
A dataframe peaklist of co-detected DIA analysis.
NPA reference xlsxAnalyzer
Description
NPA reference xlsxAnalyzer
Usage
NPA_reference_xlsxAnalyzer(ref_xlsx_file, input_path_hrms = NULL, PARAM = NULL,
PARAM_ID = "", checkpoint_parameter = TRUE)
Arguments
ref_xlsx_file |
ref_xlsx_file |
input_path_hrms |
input_path_hrms |
PARAM |
PARAM |
PARAM_ID |
PARAM_ID |
checkpoint_parameter |
checkpoint_parameter |
Value
ref_table |
ref_table |
PARAM |
PARAM |
checkpoint_parameter |
checkpoint_parameter |
FSA NPA Workflow
Description
This function runs the NPA analysis.
Usage
NPA_workflow(PARAM_NPA)
Arguments
PARAM_NPA |
PARAM_NPA |
Value
This function stores .Rdata and .csv data from dataframe peaklist of co-detected NPA analysis.
Examples
s_path <- system.file("extdata", package = "IDSL.NPA")
SSh1 <- paste0(s_path,"/NPA_parameters.xlsx")
## To see the results, use a known folder instead of the `tempdir()` command
temp_wd <- tempdir()
temp_wd_zip <- paste0(temp_wd, "/idsl.npa_testfile.zip")
spreadsheet <- readxl::read_xlsx(SSh1, sheet = "NPA")
PARAM_NPA <- cbind(spreadsheet[, 2], spreadsheet[, 4])
download.file(paste0("https://github.com/idslme/IDSL.NPA/blob/main/",
"NPA_educational_files/idsl.npa_testfile.zip?raw=true"),
destfile = temp_wd_zip, mode = "wb")
unzip(temp_wd_zip, exdir = temp_wd)
PARAM_NPA[2, 2] <- "NO"
PARAM_NPA[4, 2] <- temp_wd
PARAM_NPA[8, 2] <- temp_wd
## To ensure `PARAM_NPA` is consistent with the `NPA_workflow`
PARAM_NPA <- NPA_xlsxAnalyzer(PARAM_NPA)
##
NPA_workflow(PARAM_NPA)
xlsx Analyzer for NPA analysis
Description
This function processes the spreadsheet of the NPA spreadsheet tab to ensure the parameter inputs are in agreement with requirements of the NPA analysis.
Usage
NPA_xlsxAnalyzer(spreadsheet)
Arguments
spreadsheet |
NPA spreadsheet tab |
Value
parameters to feed the 'NPA_workflow' function.