.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH MAC3_CMBREPS "1" "February 2024" "macs3 cmbreps 3.0.1" "User Commands"
.SH NAME
mac3_cmbreps \- Model\-based Analysis for ChIP\-Sequencing
.SH DESCRIPTION
usage: macs3 cmbreps [\-h] \fB\-i\fR IFILE [IFILE ...] [\-m {fisher,max,mean}]
.IP
[\-\-outdir OUTDIR] \fB\-o\fR OFILE [\-\-verbose VERBOSE]
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-i\fR IFILE [IFILE ...]
MACS score in bedGraph for each replicate. Require at
least 2 files such as '\-i A B C D'. REQUIRED
.TP
\fB\-m\fR {fisher,max,mean}, \fB\-\-method\fR {fisher,max,mean}
Method to use while combining scores from replicates.
1) fisher: Fisher's combined probability test. It
requires scores in ppois form (\fB\-log10\fR pvalues) from
bdgcmp. Other types of scores for this method may
cause cmbreps unexpected errors. 2) max: take the
maximum value from replicates for each genomic
position. 3) mean: take the average value. Note,
except for Fisher's method, max or mean will take
scores AS IS which means they won't convert scores
from log scale to linear scale or vice versa.
.TP
\fB\-\-outdir\fR OUTDIR
If specified all output files will be written to that
directory. Default: the current working directory
.TP
\fB\-o\fR OFILE, \fB\-\-ofile\fR OFILE
Output BEDGraph filename for combined scores.
.TP
\fB\-\-verbose\fR VERBOSE
Set verbose level of runtime message. 0: only show
critical message, 1: show additional warning message,
2: show process information, 3: show debug messages.
DEFAULT:2