import useBaseUrl from '@docusaurus/useBaseUrl'; import ThemedImage from '@theme/ThemedImage';

MSPC classifies peaks under Background, Weak, Stringent, Confirmed, Discarded, True-Positive, and False-Positive categories. (Refer to method description for details.) The following figure is a schematic view of these categories and their relation.

<ThemedImage alt="Sets" sources={{ light: useBaseUrl('/img/sets.svg'), dark: useBaseUrl('/img/sets_dark.svg'), }} />

(The number of ERs in different sets reported in this figure, are the result of wgEncodeSydhTfbsK562CmycStdAlnRep1 and wgEncodeSydhTfbsK562CmycStdAlnRep2 (available for download from Sample Data page) comparative analysis using -r bio -w 1e-4 -s 1e-8 parameters.)

Peaks with p-value >= weak threshold.

Peaks with stringency threshold<= p-value <weak threshold.

Peaks with p-value < stringency threshold.

Peaks that:

1. are supported by at least c peaks from replicates, and
2. their combined stringency (xSquared) satisfies the given threshold: xSquared >= the inverse of the right-tailed probability of Gamma and
3. if technical replicate, passed all the tests, and if biological replicate, passed at least one test.

(see method description)

Peaks that:

1. does not have minimum required (i.e., c) supporting evidence, or
2. their combined stringency (xSquared) does not satisfy the given threshold, or
3. if technical replicate, failed a test.

The confirmed peaks that pass the Benjamini-Hochberg multiple testing correction at level alpha.

The confirmed peaks that fail Benjamini-Hochberg multiple testing correction at level alpha.

• Method description
• CLI output