tds: TopDownSet Example Data

In sgibb/topdownr: Investigation of Fragmentation Conditions in Top-Down Proteomics

TopDownSet Example Data

Description

An example data set for topdownr. It is just a subset of the myoglobin dataset available in topdownrdata::topdownrdata-package.

Usage

tds

Format

A TopDownSet with 14901 fragments (1949 rows, 351 columns).

Details

It was created as follows:

tds <- readTopDownFiles(
   topdownrdata::topDownDataPath("myoglobin"),
   ## Use an artifical pattern to load just the fasta
   ## file and files from m/z == 1211, ETD reagent
   ## target 1e6 and first replicate to keep runtime
   ## of the example short
   pattern=".*fasta.gz$|1211_.*1e6_1",
   adducts=data.frame(mass=1.008, name="zpH", to="z"),
   neutralLoss=PSMatch::defaultNeutralLoss(
       disableWaterLoss=c("Cterm", "D", "E", "S", "T")),
   tolerance=25e-6)

Source

Subset taken from the topdownrdata::topdownrdata-package package.

sgibb/topdownr documentation built on Jan. 16, 2024, 12:14 a.m.