Commit 5f620a7b authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
Browse files

separate IA to IDR - change default input counting

parent 3dca65fd
......@@ -215,18 +215,31 @@ seacr:
#
# :Parameters:
#
# - do: if unchecked, this rule is ignored.
# - rank: which column to use to rank peaks. Options: signal.value, p.value, q.value, columnIndex
# - thresh: report statistics for peaks with a global idr below this value. Default: 0.05
# - intersectionApproach: if set to 'yes', will compute the intersection approach and use it
# to select reproducible peaks. (for narrow only, correspond to the default broad approach)
# - ia_overlap: percentage of overlap between the peaks to be selected (-f parameter of bedtools intersect). Default: 0.8
#
#===============================================================================
compute_idr:
do: no
rank: 'signal.value'
thresh: 0.05
intersectionApproach: no
#===============================================================================
# Compute intersection approach on replicates
#
# :Parameters:
#
# - do: if set to 'yes', will compute the intersection approach and use it
# to select reproducible peaks. (for narrow only, correspond to the default broad approach)
# - ia_overlap: percentage of overlap between the peaks to be selected (-f parameter of bedtools intersect). Default: 0.8
#
#===============================================================================
intersectionApproach:
do: yes
ia_overlap: 0.8
......@@ -254,7 +267,7 @@ differential_analysis:
pAdjustMethod: "BH"
alpha: 0.05
batch: NULL
input_counting: yes
input_counting: no
#############################################################################
......
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