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flowchart.dot
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digraph flowchart {
data_import
[label="data_import.R\n\
Import the data from GEO"]
exploratory
[label="exploratory.r\n\
Perform exploratory analysis of the raw data"]
normalize
[label="normalize.r\n\
Normalize the data using BMIQ"]
exploratory_postNorm
[label="exploratory_postNorm.r\n\
Filter the data"]
aggregate_raw_norm_filter
[label="aggregate_raw_norm_filter.R\n\
Group probes into CpG islands before and after\n\
normalizing and filtering the data"]
aggregate
[label="aggregate.R\n\
Group probes into CpG islands after\n\
normalizing and filtering the data"]
hcluster
[label="hcluster.R\n\
Perform hierarchical clustering of the samples"]
lme
[label="lme_all.R\n\
Fit a linear mixed-effects model, and identify differentially\n\
methylated CpG islands for ALL vs control"]
lme_plp
[label="lme_plp.R\n\
Fit a linear mixed-effects model, and identify differentially\n\
methylated CpG islands for APL vs control"]
lme_both
[label="Table of differentially methylated CpG islands"]
differential_methylation_figures
[label="differential_methylation_figures.R\n\
Produce a heat map of probes in top 10 Islands\n\
and a Venn diagram of overlap of top islands"]
topGO
[label="topGO.R\n\
Identify enriched Gene Ontology terms"]
data_import -> exploratory
data_import -> normalize -> exploratory_postNorm -> aggregate
data_import -> aggregate_raw_norm_filter
normalize -> aggregate_raw_norm_filter
exploratory_postNorm -> aggregate_raw_norm_filter
aggregate_raw_norm_filter -> hcluster
aggregate -> lme -> lme_both
aggregate -> lme_plp -> lme_both
lme_both -> differential_methylation_figures
lme_both -> topGO
}