DIAlignR

DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.

Documentation

For documentation please see our vignette.

Developing C++ code

cd DIAlignR
mkdir build && cd build
cmake -B. -H.. 
make clean && make && make test
make runTest3
cd ..

Documenting C++ code

sudo apt install doxygen doxygen-gui 
sudo apt install graphviz
cd DIAlignR
cd src
doxygen doc/Doxyfile

Installing Rcompression

devtools::install_github("omegahat/Rcompression")

Docker

Pull image

docker push singjust/dialignr:2.0.0

Build image

docker build --no-cache -t singjust/dialignr:2.0.0 .

Run Command

$docker run -it --rm -v `pwd`:/data singjust/dialignr:2.0.0

Name:
        Run DIAlignR's alignTargetedRuns via the Command Line

    Usage:
        Rscript alignTargetedRuns_cli.R --dataPath=/data/ [args] | --help

        Example: Rscript alignTargetedRuns_cli.R --dataPath=/data/osw/ --params=context:experiment-wide,maxFdrQuery:0.01

        Example2: Rscript alignTargetedRuns_cli.R --dataPath=/data/osw/ --oswMerged=FALSE --params=context:experiment-wide,maxFdrQuery:0.01 --runs=run0,run1,run2 --peps=0,1 --applyFun=BiocParallel::bplapply --regBioCP=BiocParallel::register(BiocParallel::MulticoreParam(workers=4,progressbar=TRUE))

    Options:
        --dataPath: path to xics and osw directory.
        --outFile: name of the output file.
        --oswMerged: TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
        --params: Parameters for the alignment functions generated from DIAlignR::paramsDIAlignR(). Separate keys and values using a ':', and separate parameters using ','. Example: --params=context:experiment-wide,maxFdrQuery:0.01,fitEMG:TRUE
        --runs: names of xics file without extension. Separate runs using ','. Example: --runs=run0,run1,run2
        --refRun: reference for alignment. If no run is provided, m-score is used to select reference run.
        --peps: ids of peptides to be aligned. If NULL, align all peptides. Separate peptide ids using ','. Example--peps=1,2,3
        --appyFun: value must be either lapply or BiocParallel::bplapply.
        --regBioCP: If using BiocParallel::bplapply, register cores to use. Example: --regBioCP=BiocParallel::register(BiocParallel::MulticoreParam(workers=4,progressbar=TRUE)) . Make sure there are no spaces in this command
        --help: Display this help message

Example

docker run -it --rm -v `pwd`:/data singjust/dialignr:2.0.0 --dataPath=/data/ --outFile=/data/dialignr

Snakemake

To run the snakemake workflow, you need to ensure you have snakemake and singularity installed.

To change parameters for your experiment, edit the input, output and parameters in the snakemake/Snakefile.dialignr file.

Run Command

Snakefile.dialignr will need to be in the same directory as cmd.sh

$cd snakemake
$bash cmd.sh

Citation

If you use the provided algorithms or the package, please cite our paper:

Gupta S, Ahadi S, Zhou W, Röst H. "DIAlignR Provides Precise Retention Time Alignment Across Distant Runs in DIA and Targeted Proteomics." Mol Cell Proteomics. 2019 Apr;18(4):806-817. doi: https://doi.org/10.1074/mcp.TIR118.001132 Epub 2019 Jan 31.

CNPN 2018 Poster doi: https://doi.org/10.6084/m9.figshare.6200837.v1
HUPO 2018 Poster doi: https://doi.org/10.6084/m9.figshare.7121696.v2