Command: call¶
Call peaks in a .ccf file
Required parameters:
-i, –input INPUT: input .ccf file
output: output bed file
Either:
-p, –pValueCutoff PVALUECUTOFF: p-value cutoff (NOTE: This is a straight cutoff and will not take into account multiple hypothesis correction!), OR
-a, –alpha ALPHA: alpha for multiple hypothesis correction (must be between 0 and 1) AND
–correction CORRECTION: if alpha provided, need to specificity method of multiple hypothesis correction. See statsmodels.stats.multitest for a complete list of choices (default: bonferroni)
-bg, –background BACKGROUND: Background .ccf file
Optional parameters:
-r, –regions REGIONS: Regions over which to normalize event counts; should be supplied as a BED file. If not provided, the input file will be segmented using Bayesian blocks. (all options from blockify segment are available)
–intermediate INTERMEDIATE: Intermediate file to write verbose output (CSV format)
-d, –distance DISTANCE: Merge features closer than this distance (bp)
–min MIN: Report peaks larger than this cutoff (bp)
–max MAX: Report peaks smaller than this cutoff (bp)
-t, –tight: Shrink peak boundaries to overlap data points
-c, –pseudocount PSEUDOCOUNT: Pseudocount for background regions (default: 1)