[DEFAULT]

[column_names]
batch = 
group = Sample_Group
name = Sample_Name
sex = Sex
age = 

[probe_filter]
find_failures = y
cross_reactive_probes = y
find_snps_chen = y
find_extremes = n
find_chromosomes = n
find_snps_minfi = y

[find_failures]
padjust_method = none
pvalue = 0.05
percent_failed_threshold = 0.25

[cross_reactive_probes]

[find_snps_chen]
minimal_distance_to_SNPs = 2
minimal_minor_allele_frequency = 0.5

[find_chromosomes]
chromosomes = chrY,chrX

[normalize]
method = Illumina

[cell_counts]
column_prefix = CellCounts.

[differential_methylated_pos]
minfi = y
limma = y
MannWhitney = y

[minfi_differential_methylated_pos]
padjust_method = fdr
pvalue = 0.05
delta_beta_threshold = 0.1

[limma_differential_methylated_pos]
padjust_method = fdr
pvalue = 0.05
delta_beta_threshold = 0.1
design_matrix_columns = Sex,CellCounts.Gran

[MannWhitney_differential_methylated_pos]
paired = n
padjust_method = fdr
pvalue = 0.05
delta_beta_threshold = 0.1

[differential_methylated_regions]
nullMethod = 
permutations = 100
delta_beta_threshold = 0.1
pvalue = 0.05
LCutoff = 3
cores = 4

[combine_differential_methylated_pos]
image_ext = png

[feature_selection]
method = none
cutoff = 2000

[enrichment_analysis]
own_file = n

[position_enrichment_minfi]

[position_enrichment_limma]

[position_enrichment_MannWhitney]

[position_enrichment_overlapping]

[position_enrichment_analysis]
assembly = hg19
collection = tfbs,Histone

[region_enrichment_analysis]
assembly = hg19
collection = tfbs,Histone

[build_model]
method = 

[impute_beta]

[apply_models]

[report]
title = Epigene 450k Analysis Report
data_type = 450k