get_ms1ft: Generates the "ms1ft" object, which is Top-Down MS1 Feature...

In EMSL-Computing/pspecterlib: PSpecteR Library - Visualization tools for top-down and bottom-up proteomics data

Generates the "ms1ft" object, which is Top-Down MS1 Feature data

Description

Reads in ms1ft from the ProMex algorithm in InformedProteomics, and associates features to protein data from the Ic_Targets file from MSPathFinderT. All of this data is used to generate the promex feature plot.

Usage

get_ms1ft(MS1FTPath, TargetsPath = NULL, TrimColumns = TRUE)

Arguments

MS1FTPath	Path to the MS1FT txt file, which is a tsv. Required.
TargetsPath	Optional path to an IC targets file which links MS1FT features to proteins. Default is NULL.
TrimColumns	A logical to indicate whether all columns or only columns relevant to promex_feature_plot should be returned. Default is TRUE.

Details

The data.table outputted by this function contains many columns. Listed below are the main ones.

FeatureID	An identified mass across elution (retention) times is given a feature ID, typically a single number.
MinElutionTime	The smallest retention time of the feature
MaxElutionTime	The largest retention time of the feature
MonoMass	The monoisotopic mass of the feature.
Abundance	The relative abundance of the feature.
ProteinName	If the Targets file is provided, the name of the protein associated to that feature.

Examples

## Not run: 

# Test top down data
tmpdir <- tempdir()
download.file("https://raw.githubusercontent.com/EMSL-Computing/PSpecteR/master/pspecter_container/TestFiles/TopDown/TopDown.ms1ft",
              file.path(tmpdir, "TopDown.ms1ft"))
download.file("https://raw.githubusercontent.com/EMSL-Computing/PSpecteR/master/pspecter_container/TestFiles/TopDown/TopDown_IcTarget.tsv",
              file.path(tmpdir, "TopDown_IcTarget.tsv"))

# Generate object
MS1FT <- get_ms1ft(MS1FTPath = file.path(tmpdir, "TopDown.ms1ft"),
                   TargetsPath = file.path(tmpdir, "TopDown_IcTarget.tsv"))


## End(Not run)

EMSL-Computing/pspecterlib documentation built on Jan. 28, 2024, 8:13 p.m.