This is an R package for reading MaxQuant protein and peptide data, currently from label-free experiments only.
# Get the the development version from GitHub:
# install.packages("devtools")
devtools::install_github("slurmclassic/maxquant.tools")
# Read a proteinGroups.txt file.
protein_group_data = readMaxQuantProteinMeasurements('examples/proteinGroups.txt')
# Read a peptides.txt file.
peptide_data = readMaxQuantPeptideMeasurements('examples/peptides.txt')
# Merge two protein group datasets.
a = readMaxQuantProteinMeasurements('examples/proteinGroups1.txt')
b = readMaxQuantProteinMeasurements('examples/proteinGroups2.txt')
merged_dataset = a + b
# Or use the underlying merge function with a list of datasets.
merged_dataset = mergeMaxQuantProteinGroupsResults(list(a, b), 'Merged Dataset Name')
# Merging two peptide datasets is very similar.
a = readMaxQuantPeptideMeasurements('examples/peptides1.txt')
b = readMaxQuantPeptideMeasurements('examples/peptides2.txt')
merged_dataset = a + b
# Or use the underlying merge function with a list of datasets.
merged_dataset = mergeMaxQuantPeptideResults(list(a, b), 'Merged Dataset Name')
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