Example: DMRs¶

---

Example: BAT_DMRcalling¶

(USAGE BAT_DMRcalling)

Command¶

BAT_DMRcalling -q data/example_metilene_control_case.txt -o DMRs/metilene -a control -b case

Output files¶

DMRs/metilene.out
DMRs/metilene_qval.0.05.out
DMRs/metilene_qval.0.05.bedgraph
DMRs/metilene_qval.0.05.bed
DMRs/metilene_qval.0.05.pdf

View¶

$ head -3 DMRs/metilene.out
chr19   10624503        10624742        3.3e-16 -0.383986       37      4.3e-14 1.5e-19   0.25041   0.63439
chr19   10625238        10625388        6.9e-07 -0.194231       26      4.9e-14 3.1e-10   0.09375   0.28798
chr19   10625393        10625445        9.1e-06 -0.334423       13      4.6e-12 4.1e-09   0.14346   0.47788

$ head -3 DMRs/metilene_qval.0.05.out
chr19   10624503        10624742        3.3e-16 -0.383986       37      0.25041 0.63439
chr19   10625238        10625388        6.9e-07 -0.194231       26      0.09375 0.28798
chr19   10625393        10625445        9.1e-06 -0.334423       13      0.14346 0.47788

$ head -3 DMRs/metilene_qval.0.05.bedgraph
chr19   10624503        10624742        -0.383986
chr19   10625238        10625388        -0.194231
chr19   10625393        10625445        -0.334423

$ head -3 DMRs/metilene_qval.0.05.bed
chr19   10624503        10624742        DMR_1   hypomethylated
chr19   10625238        10625388        DMR_2   hypomethylated
chr19   10625393        10625445        DMR_3   hypomethylated

DMRs/metilene_qval.0.05.pdf

(top)

---

Example: BAT_correlating ¶

(USAGE BAT_correlating)

Commands¶

Create input for BAT_correlating

bedtools intersect -wa -wb -a DMRs/metilene_qval.0.05.bed -b genomes/hg19/gene.bed | cut -f1-3,9 >DMRs/DMR_gene.txt
ls data/*.bw | grep -v "mean" | grep -v "diff" | sed 's/\t/\n/' >DMRs/methylation_files.list
ls expression/* | sed 's/\t/\n/' >DMRs/expression_files.list
echo -e 'S1\tcontrol\nS2\tcontrol\nS3\tcontrol\nS4\tcontrol\nS5\tcase\nS6\tcase\nS7\tcase\nS8\tcase' >DMRs/sample_to_group.txt

Run BAT_correlating:

BAT_correlating -b DMRs/DMR_gene.txt -e DMRs/expression_files.list -m DMRs/methylation_files.list -g DMRs/sample_to_group.txt -i control,case -o DMRs/correlation

Output files¶

...
correlation.txt
DMRs/correlation_chr19:11144943-11145419_ENSG00000127616.pdf
...

View¶

$ head -3 correlation.txt
plot.pdf    ENSG_ID methylation_region  adj.R2  rho rho.p-val
DMRs/correlation_chr19:10858170-10858760_ENSG00000079805.pdf    ENSG00000079805 chr19:10858170-10858760 0.34    0.83    0.0114
DMRs/correlation_chr19:10928642-10928813_ENSG00000079805.pdf    ENSG00000079805 chr19:10928642-10928813 0.69    0.85    0.0075

DMRs/correlation_chr19:10625244-10625340_ENSG00000180739.pdf

---

(top)