MACS3.Signal.CallPeakUnit module

Compute MACS3 peak-calling scores and helper statistics.

This code is free software; you can redistribute it and/or modify it under the terms of the BSD License (see the file LICENSE included with the distribution).

class MACS3.Signal.CallPeakUnit.CallerFromAlignments

Bases: object

Compute pileups, scores, and peaks from FWTrack/PETrack alignments.

treat

Treatment track (FWTrack or PETrackI/PETrackII).

ctrl

Control track (FWTrack or PETrackI/PETrackII).

d

Fragment extension size for treatment (unused in PE mode).

ctrl_d_s

Fragment extension size for control.

treat_scaling_factor

Scaling factor for treatment.

ctrl_scaling_factor_s

Scaling factors for control.

lambda_bg

Minimum local bias to fill missing values.

chromosomes

Common chromosome names in treat/control.

pseudocount

Pseudocount used for logLR/FE/logFE calculations.

bedGraph_filename_prefix

Prefix for pileup/lambda bedGraph outputs.

end_shift

Shift applied to read ends before extension.

trackline

Whether to emit UCSC track lines in bedGraph outputs.

save_bedGraph

Whether to save pileup/lambda bedGraph files.

save_SPMR

Whether to save pileup normalized per million reads.

no_lambda_flag

Whether to ignore local lambda (use global only).

PE_mode

Whether treatment is paired-end.

call_broadpeaks(scoring_function_symbols, lvl1_cutoff_s, lvl2_cutoff_s, min_length=200, lvl1_max_gap=50, lvl2_max_gap=400, cutoff_analysis=False)

This function try to find enriched regions within which, scores are continuously higher than a given cutoff for level 1, and link them using the gap above level 2 cutoff with a maximum length of lvl2_max_gap.

Parameters:

  • scoring_function_symbols (list) – Symbols for score functions. Use 'p' (pscore), 'q' (qscore), 'f' (fold change), or 's' (subtraction). Example: ['p', 'q'].

  • lvl1_cutoff_s (list) – Cutoffs for highly enriched regions.

  • lvl2_cutoff_s (list) – Cutoffs for linkage regions.

  • min_length (cython.int) – Minimum peak length.

  • lvl1_max_gap (cython.int) – Maximum gap to merge nearby peaks.

  • lvl2_max_gap (cython.int) – Maximum length of linkage regions.

  • cutoff_analysis (bool) – Whether to compute cutoff-vs-peak metrics.

Returns:

(PeakIO, BroadPeakIO) for level-1 peaks and broad regions.

Return type:

tuple

Examples

lvl1, broad = caller.call_broadpeaks(['p'], [5.0], [2.0])
call_peaks(scoring_function_symbols, score_cutoff_s, min_length=200, max_gap=50, call_summits=False, cutoff_analysis=False)

Call narrow peaks for all chromosomes.

Parameters:

  • scoring_function_symbols (list) – Symbols for score functions. Use 'p' (pscore), 'q' (qscore), 'f' (fold change), or 's' (subtraction). Example: ['p', 'q'].

  • score_cutoff_s (list) – Cutoff values corresponding to scoring_function_symbols.

  • min_length (cython.int) – Minimum peak length.

  • max_gap (cython.int) – Maximum gap of insignificant regions within a peak.

  • call_summits (bool) – Whether to call sub-peaks (summits).

  • cutoff_analysis (bool) – Whether to compute cutoff-vs-peak metrics.

Returns:

Collection of called peaks.

Return type:

PeakIO

Examples

peaks = caller.call_peaks(['p'], [5.0], min_length=200)
destroy()

Remove temporary pileup files created during peak calling.

enable_trackline()

Enable UCSC track line output when writing bedGraphs.

set_pseudocount(pseudocount)

Update the pseudocount used in scoring.