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Description:
  Using combined evidence from replicates to evaluate ChIP-seq and single-cell peaks.
  Documentation: https://genometric.github.io/MSPC/
  Source Code:   https://github.com/Genometric/MSPC
  Publications:  https://genometric.github.io/MSPC/publications

MSPC mspc is a command line interface to the MSPC method; it parses input datasets (e.g., BED files), invokes the method to analyze them, and persists the results.

The mspc is a cross-platform command-line application, and can be invoked from any shell, such as Windows PowerShell, Linux shell, or Mac OS Terminal. A basic mspc invocation takes four arguments (i.e., input, replicate type, and stringency and weak thresholds), runs MSPC Core, and persists results. For instance, see the following sample execution:

$ dotnet .\mspc.dll -i rep1.bed -i rep2.bed \
                    -r bio -w 1e-4 -s 1e-8

Output:

.::........Parsing Samples.........::.
     #                Filename    Read peaks#     Min p-value     Mean p-value    Max p-value
----    --------------------    -----------     -----------     ------------    -----------
 1/2                    rep1         53,697      2.239E-074       1.085E-003     1.000E-002
 2/2                    rep2         37,717      5.370E-301       1.520E-004     9.550E-003

.::.......Analyzing Samples........::.

[1/4] Initializing
[2/4] Processing samples
  └── 60,004/60,004     (100.00%) peaks processed
[3/4] Performing Multiple testing correction
[4/4] Creating consensus peaks set

.::.........Saving Results.........::.


.::.......Summary Statistics.......::.

   #                Filename    Read peaks#     Background          Weak        Stringent       Confirmed       Discarded       TruePositive    FalsePositive
----    --------------------    -----------     ----------      --------        ---------       ---------       ---------       ------------    -------------
 1/2                    rep1         53,697         47.05%        42.95%           10.01%          26.84%          26.12%             26.84%            0.00%
 2/2                    rep2         37,717         16.30%        50.35%           33.35%          43.48%          40.22%             43.48%            0.00%

.::.....Consensus Peaks Count......::.

17,290

All processes successfully finished

In this example, MSPC is called using two samples (i.e., -i rep1.bed -i rep2.bed), which are considered as biological replicates (-r bio) with 1E-4 and 1E-8 thresholds on p-values defining stringent and weak peaks respectively.

Once executed, MSPC reports the following (see the Output section for details):

For each parsed sample, it reports the number of parsed peaks, minimum and maximum p-values parsed from the file;
Reports analysis steps;
Summary statistics containing the following information:
- per-sample summary statistics that informs the number of analyzed peaks, and what percentage of these peaks are identified as Stringent, Weak, Confirmed, and etc. (see sets description).
  info
  The percentages reported for Stringent, Weak, and Background sets, should add-up to 100%; however, the percentage reported for Confirmed and Discarded is not expected to add-up to 100% if the percentage of Background set is not 0%. Similarly, the percentages reported for TruePositive and FalsePositive sets will not add-up to 100% if the percentage of Background and Discarded is not 0% (see sets description).
Number of consensus peaks.

See Also​

See Also