Example data set for proteus
package. It comes from a label-free MS/MS
experiment in two biological conditions (called A and B) and seven replicates each. The data come
from an unpublished experiment by Katharina Trunk, Sarah Coulthurst, Julien Peltier and Matthias Trost.
Nine objects from different stages of data processing:
evi
Pre-processed evidence data (data frame)
meta
Metadata (data frame)
meta.clean
Clean metadata (data frame)
pepdat
Peptide data (proteusData
object)
pepdat.clean
Clean peptide data (proteusData
object)
prodat
Protein data (proteusData
object)
annotations
Protein annotations downloaded from UniProt
annotations.id
Protein annotations ready for merging
evitab.example
Example fragment of evidence data
This package also contains the full original evidence file, peptides file, proteinGroups file and formatted metadata file (see examples below).
1 2 3 4 5 6 7 8 9 10 | library(proteusLabelFree)
data(proteusLabelFree)
meta
head(pepdat$tab)
head(prodat$tab)
evidenceFile <- system.file("extdata", "evidence.txt.gz", package="proteusLabelFree")
peptidesFile <- system.file("extdata", "peptides.txt.gz", package="proteusLabelFree")
proteinGroupsFile <- system.file("extdata", "proteinGroups.txt.gz", package="proteusLabelFree")
metadataFile <- system.file("extdata", "metadata.txt", package="proteusLabelFree")
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