### This is a sample configuration file
## data section is used to describe some general configurations of experimental design
[data]
## Experimental title. Temporary R results will be saved under this name.
Title=Affy_test
## If the format line is missing by default program thinks the inputs are CEL files.
## Alternative option is "text", which is for data from other platform.
Format=cel
## Bpmap files used. This is only useful when input files are Affymetrix CEL files
Bpmap = /dir/to/CEL/Mm_PromPR_v02-1_NCBIv36.bpmap
## Location for CEL files
CelFolder =/dir/to/CEL
## Whether the CEL files are paired. 1 means paired, 0 means unpaired
Pair = 0
## Working folder. Both temporary and final results will be written to this folder.
WorkFolder=.

## list of CEL files, each row is for a condition. 
## If the CEL files are paired, files need to be specified in 
## orders such as IP1, control1, IP2, control2, etc.
## If they are not paired, a "Group" section need to be specified. 
## Left hand side of the "=" is the condition name, 
## which will be used for output file names. 
## When input files are not from Affymetrix this section will be omitted.
[cel]
cond1=Cond1_IP1.CEL Cond1_IP2.CEL Cond1_CT1.CEL Cond1_CT2.CEL
cond2=Cond2_IP1.CEL Cond2_IP2.CEL Cond2_CT1.CEL Cond2_CT2.CEL
cond3=Cond3_IP1.CEL Cond3_IP2.CEL Cond3_CT1.CEL Cond3_CT2.CEL
cond4=Cond4_IP1.CEL Cond4_IP2.CEL Cond4_CT1.CEL Cond4_CT2.CEL

## For non-paired experiments. Number of lines and left hands of "=" must 
## match the [cel] section. In this example cond1=1100 means under [cel]
## section, first 2 CEL files for cond1 condition are from IP channels 
## and the last 2 are from control channels.
[Group]
cond1=1100
cond2=1100
cond3=1100
cond4=1100

## Parameters for peak finding. 
[peak finding]
## Maximum gap between two adjecent probes allowed in a peak.
maxGap=300
## Minimum number of probes allowed for a peak.
MinProbe=6
## Length of a potential binding region.
candidateLength=1000
## Allowable peak length with in the potential binding regions. 
bumpLength=300 500 700 900
## FDR cutoff values for defining a peak list.
FDRcutoff=0.2
## Method to compute FDR for a peak list.
## 0: compute from posterior probabilities (faster and recommended);
## 1: empirically estimate from data using negative intensities.
computeFDR=0