# Protein Quantification in Mass Spectrometry-Based Proteomics

## Documentation for package ‘iq’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

connected_component | Group connected samples
create_protein_list | Creating a list of matrices of fragment ion intensities for all proteins
create_protein_table | Protein quantification for a list of proteins
extract_annotation | Protein annotation extraction
fast_MaxLFQ | The MaxLFQ algorithm
fast_preprocess | Data filtering and normalization
fast_read | Reading data from an input file
long_format_to_iq_format | Long format input data to iq format
maxLFQ | The MaxLFQ algorithm for protein quantification
meanInt | The meanInt algorithm for protein quantification
median_polish | A wrapper for the R implementation of the median polish algorithm
plot_protein | Plotting the underlying quantitative data for a protein
preprocess | Data preprocessing for protein quantification
process_iq_format | Process data in the iq format
process_long_format | Long format to a wide format table using the MaxLFQ algorithm
process_matrix | Process individual matrix
process_wide_format | Merging rows with identical values in a particular column in a table
rescale | Rescale relative quantification
spikeins | An example dataset of 12 spike-in proteins
topN | The topN algorithm for protein quantification