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lijingya / ELMER

Enhancer Linking by Methylation/Expression Relationship (ELMER) is package to identify tumor-specific changes in DNA methylation within distal enhancers, and link these enhancers to downstream target genes
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Error in get.TFs when we have only one enriched motif #13

Open tiagochst opened 8 years ago

tiagochst commented 8 years ago

When only one enriched motif is found by get.enriched.motif, the function get.TFs gives an error. Making the lower.OR lower to get two motifs solves the problem.

1 motifs are enriched.
[1] "get.TFs"
 Hide Traceback

 Rerun with Debug
 Error in gzfile(file) : invalid 'description' argument 
3 gzfile(file) 
2 load(enriched.motif, envir = newenv) 
1 get.TFs(mee = mee, enriched.motif = enriched.motif, dir.out = dir.out, 
    cores = 8, label = i) 
> enriched.motif
      E2F1        
 [1,] "cg15589153"
 [2,] "cg15551105"
 [3,] "cg00793280"
 [4,] "cg25439496"
 [5,] "cg06003656"
 [6,] "cg06610849"
 [7,] "cg13337047"
 [8,] "cg26274580"
 [9,] "cg15027907"
[10,] "cg15799395"
[11,] "cg19681029"
[12,] "cg25214923"
[13,] "cg27305735"
> enriched.motif <- get.enriched.motif(probes=Sig.probes.paired[,1],
+                                              dir.out=dir.out, label=i,
+                                              background.probes = probe$name,
+                                              lower.OR = 1.00)
2 motifs are enriched.
> TF <- get.TFs(mee=mee,
+                       enriched.motif=enriched.motif,
+                       dir.out=dir.out,
+                       cores=8, label= i)
> enriched.motif
$E2F1
 [1] "cg15589153" "cg15551105" "cg00793280" "cg25439496" "cg06003656"
 [6] "cg06610849" "cg13337047" "cg26274580" "cg15027907" "cg15799395"
[11] "cg19681029" "cg25214923" "cg27305735"

$UA3
 [1] "cg15589153" "cg00793280" "cg19137348" "cg27221053" "cg10649525"
 [6] "cg26274580" "cg15837212" "cg26654934" "cg08489324" "cg15027907"
[11] "cg15799395" "cg25214923" "cg26654934" "cg27305735"